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.gitattributes
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@@ -1492,3 +1492,4 @@ data/files/A007V/topology.tpr filter=lfs diff=lfs merge=lfs -text
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data/files/A00DO/trajectory.xtc filter=lfs diff=lfs merge=lfs -text
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data/files/A007Z/topology.tpr filter=lfs diff=lfs merge=lfs -text
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data/files/A00EM/topology.tpr filter=lfs diff=lfs merge=lfs -text
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data/files/A00DO/trajectory.xtc filter=lfs diff=lfs merge=lfs -text
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data/files/A007Z/topology.tpr filter=lfs diff=lfs merge=lfs -text
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data/files/A00EM/topology.tpr filter=lfs diff=lfs merge=lfs -text
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data/files/all_records.jsonl filter=lfs diff=lfs merge=lfs -text
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data/files/A00FR/project.json
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| 1 |
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{
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"accession": "A00FR",
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"published": true,
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"metadata": {
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| 5 |
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"NAME": "Dynarepo 7LR4",
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"DESCRIPTION": "Antigen from Zhao test set, Classical MD simulations, 3 replicates of 500 ns",
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| 7 |
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"AUTHORS": [
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"Omid Mokhtari",
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"Hamed Khakzad",
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"Yasaman Karami"
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],
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"TYPE": "trajectory",
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"METHOD": "Classical MD",
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"LICENSE": "Apache License 2.0",
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"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
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data/files/A00FR/records.jsonl
ADDED
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data/files/A00FS/project.json
ADDED
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@@ -0,0 +1,158 @@
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| 1 |
+
{
|
| 2 |
+
"accession": "A00FS",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
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"NAME": "Dynarepo 7LVW",
|
| 6 |
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"DESCRIPTION": "Antigen from Zhao test set, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
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],
|
| 12 |
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"GROUPS": [
|
| 13 |
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|
| 14 |
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],
|
| 15 |
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"CONTACT": "[email protected]",
|
| 16 |
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"PROGRAM": "GROMACS",
|
| 17 |
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"VERSION": "2024.2",
|
| 18 |
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"TYPE": "trajectory",
|
| 19 |
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"METHOD": "Classical MD",
|
| 20 |
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"LICENSE": "Apache License 2.0",
|
| 21 |
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"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
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"CITATION": "DynaRepo citation",
|
| 23 |
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"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
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"LINKS": null,
|
| 25 |
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"PDBIDS": [
|
| 26 |
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"7LVW"
|
| 27 |
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],
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| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
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"REFERENCES": [
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| 30 |
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"P03420"
|
| 31 |
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],
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| 32 |
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"INPUT_LIGANDS": null,
|
| 33 |
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| 34 |
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| 35 |
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"PROTSEQ": [
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| 36 |
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| 37 |
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],
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| 38 |
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"NUCLSEQ": [],
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| 39 |
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|
| 40 |
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"Fusion glycoprotein F0",
|
| 41 |
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"Fusion glycoprotein F2",
|
| 42 |
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"Fusion glycoprotein F1",
|
| 43 |
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"Fusion peptide",
|
| 44 |
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"Cleavage; by host furin-like protease"
|
| 45 |
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],
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| 46 |
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|
| 47 |
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|
| 48 |
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|
| 49 |
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|
| 50 |
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"FF": [
|
| 51 |
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"CHARMM36m"
|
| 52 |
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],
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| 53 |
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"WAT": "TIP3P",
|
| 54 |
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| 55 |
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| 56 |
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| 57 |
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},
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| 89 |
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| 129 |
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"clusters_00_screenshot_18.jpg",
|
| 130 |
+
"clusters_00_screenshot_19.jpg",
|
| 131 |
+
"clusters_00_screenshot_20.jpg",
|
| 132 |
+
"pocket_01.pdb",
|
| 133 |
+
"pocket_02.pdb",
|
| 134 |
+
"pocket_03.pdb"
|
| 135 |
+
],
|
| 136 |
+
"analyses": [
|
| 137 |
+
"mem-map",
|
| 138 |
+
"clusters",
|
| 139 |
+
"clusters-00",
|
| 140 |
+
"fluctuation",
|
| 141 |
+
"pca",
|
| 142 |
+
"pockets",
|
| 143 |
+
"rgyr",
|
| 144 |
+
"rmsd-pairwise",
|
| 145 |
+
"rmsd-perres",
|
| 146 |
+
"rmsds",
|
| 147 |
+
"sasa",
|
| 148 |
+
"tmscores"
|
| 149 |
+
],
|
| 150 |
+
"updateDate": "2025-07-23T12:42:47.342Z",
|
| 151 |
+
"mdcount": 3,
|
| 152 |
+
"mdIndex": 0,
|
| 153 |
+
"mdNumber": 1,
|
| 154 |
+
"refframe": 0,
|
| 155 |
+
"internalId": "687fa3f46b22a9339ea8194a",
|
| 156 |
+
"creationDate": "2025-07-22T14:45:08.000Z",
|
| 157 |
+
"identifier": "A00FS"
|
| 158 |
+
}
|
data/files/A00FS/records.jsonl
ADDED
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@@ -0,0 +1,3 @@
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| 1 |
+
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| 2 |
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| 3 |
+
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| 1 |
+
{
|
| 2 |
+
"accession": "A00FT",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 7LZP",
|
| 6 |
+
"DESCRIPTION": "Antigen from Zhao test set, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"CONTACT": "[email protected]",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
+
"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
+
"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
+
"CITATION": "DynaRepo citation",
|
| 23 |
+
"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
+
"LINKS": null,
|
| 25 |
+
"PDBIDS": [
|
| 26 |
+
"7LZP"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P0DPI1"
|
| 31 |
+
],
|
| 32 |
+
"INPUT_LIGANDS": null,
|
| 33 |
+
"LIGANDS": [],
|
| 34 |
+
"LIGANDNAMES": null,
|
| 35 |
+
"PROTSEQ": [
|
| 36 |
+
"PFVNKQFNYKDPVNGVDIAYIKIPNVGQMQPVKAFKIHNKIWVIPERDTFTNPEEGDLNPPPEAKQVPVSYYDSTYLSTDNEKDNYLKGVTKLFERIYSTDLGRMLLTSIVRGIPFWGGSTIDTELKVIDTNCINVIQPDGSYRSEELNLVIIGPSADIIQFECKSFGHEVLNLTRNGYGSTQYIRFSPDFTFGFEESLEVDTNPLLGAGKFATDPAVTLAHELIHAGHRLYGIAINPNRVFKVNTNAYYEMSGLEVSFEELRTFGGHDAKFIDSLQENEFRLYYYNKFKDIASTLNKAKSIVGTTASLQYMKNVFKEKYLLSEDTSGKFSVDKLKFDKLYKMLTEIYTEDNFVKFFKVLNRKTYLNFDKAVFKINIVPKVNYTIYDGFNLRNTNLAANFNGQNTEINNMNFTKLKNFTGLFEFYKLLCVRGIITSK"
|
| 37 |
+
],
|
| 38 |
+
"NUCLSEQ": [],
|
| 39 |
+
"DOMAINS": [
|
| 40 |
+
"Botulinum neurotoxin type A",
|
| 41 |
+
"Botulinum neurotoxin A light chain"
|
| 42 |
+
],
|
| 43 |
+
"FRAMESTEP": 0.1,
|
| 44 |
+
"TIMESTEP": 2,
|
| 45 |
+
"TEMP": 310,
|
| 46 |
+
"ENSEMBLE": "NPT",
|
| 47 |
+
"FF": [
|
| 48 |
+
"CHARMM36m"
|
| 49 |
+
],
|
| 50 |
+
"WAT": "TIP3P",
|
| 51 |
+
"BOXTYPE": "Dodecahedron",
|
| 52 |
+
"SYSTATS": 7045,
|
| 53 |
+
"SYSTRES": 437,
|
| 54 |
+
"PROTATS": 7045,
|
| 55 |
+
"PROTRES": 437,
|
| 56 |
+
"NUCLATS": 0,
|
| 57 |
+
"NUCLRES": 0,
|
| 58 |
+
"LIPIATS": 0,
|
| 59 |
+
"LIPIRES": 0,
|
| 60 |
+
"CARBATS": 0,
|
| 61 |
+
"CARBRES": 0,
|
| 62 |
+
"SOLVATS": 0,
|
| 63 |
+
"SOLVRES": 0,
|
| 64 |
+
"COUNCAT": 0,
|
| 65 |
+
"COUNANI": 0,
|
| 66 |
+
"COUNION": 0,
|
| 67 |
+
"INTERACTIONS": [],
|
| 68 |
+
"PBC_SELECTION": null,
|
| 69 |
+
"CHAINNAMES": null,
|
| 70 |
+
"MEMBRANES": null,
|
| 71 |
+
"CUSTOMS": null,
|
| 72 |
+
"ORIENTATION": null,
|
| 73 |
+
"PTM": [],
|
| 74 |
+
"MULTIMERIC": null,
|
| 75 |
+
"COLLECTIONS": "dynarepo",
|
| 76 |
+
"WARNINGS": [],
|
| 77 |
+
"BOXSIZEX": 10.0851,
|
| 78 |
+
"BOXSIZEY": 10.0851,
|
| 79 |
+
"BOXSIZEZ": 7.09578,
|
| 80 |
+
"mdName": "replica 1",
|
| 81 |
+
"mdAtoms": 7045,
|
| 82 |
+
"mdFrames": 5001
|
| 83 |
+
},
|
| 84 |
+
"mds": [
|
| 85 |
+
"replica 1",
|
| 86 |
+
"replica 2",
|
| 87 |
+
"replica 3"
|
| 88 |
+
],
|
| 89 |
+
"mdref": 0,
|
| 90 |
+
"files": [
|
| 91 |
+
"topology.tpr",
|
| 92 |
+
"screenshot.jpg",
|
| 93 |
+
"trajectory.bin",
|
| 94 |
+
"pca_trajectory_01.bin",
|
| 95 |
+
"pca_trajectory_02.bin",
|
| 96 |
+
"pca_trajectory_03.bin",
|
| 97 |
+
"pca_trajectory_04.bin",
|
| 98 |
+
"pca_trajectory_05.bin",
|
| 99 |
+
"pca_trajectory_06.bin",
|
| 100 |
+
"pca_trajectory_07.bin",
|
| 101 |
+
"pca_trajectory_08.bin",
|
| 102 |
+
"pca_trajectory_09.bin",
|
| 103 |
+
"pca_trajectory_10.bin",
|
| 104 |
+
"pca_trajectory_11.bin",
|
| 105 |
+
"pca_trajectory_12.bin",
|
| 106 |
+
"pca_trajectory_13.bin",
|
| 107 |
+
"pca_trajectory_14.bin",
|
| 108 |
+
"pca_trajectory_15.bin",
|
| 109 |
+
"structure.pdb",
|
| 110 |
+
"trajectory.xtc",
|
| 111 |
+
"clusters_00_screenshot_00.jpg",
|
| 112 |
+
"clusters_00_screenshot_01.jpg",
|
| 113 |
+
"clusters_00_screenshot_02.jpg",
|
| 114 |
+
"clusters_00_screenshot_03.jpg",
|
| 115 |
+
"clusters_00_screenshot_04.jpg",
|
| 116 |
+
"clusters_00_screenshot_05.jpg",
|
| 117 |
+
"clusters_00_screenshot_06.jpg",
|
| 118 |
+
"clusters_00_screenshot_07.jpg",
|
| 119 |
+
"clusters_00_screenshot_08.jpg",
|
| 120 |
+
"clusters_00_screenshot_09.jpg",
|
| 121 |
+
"clusters_00_screenshot_10.jpg",
|
| 122 |
+
"clusters_00_screenshot_11.jpg",
|
| 123 |
+
"clusters_00_screenshot_12.jpg",
|
| 124 |
+
"clusters_00_screenshot_13.jpg",
|
| 125 |
+
"clusters_00_screenshot_14.jpg",
|
| 126 |
+
"clusters_00_screenshot_15.jpg",
|
| 127 |
+
"clusters_00_screenshot_16.jpg",
|
| 128 |
+
"clusters_00_screenshot_17.jpg",
|
| 129 |
+
"clusters_00_screenshot_18.jpg",
|
| 130 |
+
"clusters_00_screenshot_19.jpg",
|
| 131 |
+
"pocket_01.pdb",
|
| 132 |
+
"pocket_02.pdb",
|
| 133 |
+
"pocket_03.pdb",
|
| 134 |
+
"pocket_04.pdb",
|
| 135 |
+
"pocket_05.pdb",
|
| 136 |
+
"pocket_06.pdb",
|
| 137 |
+
"pocket_07.pdb",
|
| 138 |
+
"pocket_08.pdb",
|
| 139 |
+
"pocket_09.pdb",
|
| 140 |
+
"pocket_10.pdb"
|
| 141 |
+
],
|
| 142 |
+
"analyses": [
|
| 143 |
+
"mem-map",
|
| 144 |
+
"clusters",
|
| 145 |
+
"clusters-00",
|
| 146 |
+
"fluctuation",
|
| 147 |
+
"pca",
|
| 148 |
+
"pockets",
|
| 149 |
+
"rgyr",
|
| 150 |
+
"rmsd-pairwise",
|
| 151 |
+
"rmsd-perres",
|
| 152 |
+
"rmsds",
|
| 153 |
+
"sasa",
|
| 154 |
+
"tmscores"
|
| 155 |
+
],
|
| 156 |
+
"updateDate": "2025-07-23T12:42:50.574Z",
|
| 157 |
+
"mdcount": 3,
|
| 158 |
+
"mdIndex": 0,
|
| 159 |
+
"mdNumber": 1,
|
| 160 |
+
"refframe": 3,
|
| 161 |
+
"internalId": "687fa52f239c11c57d64e3e1",
|
| 162 |
+
"creationDate": "2025-07-22T14:50:23.000Z",
|
| 163 |
+
"identifier": "A00FT"
|
| 164 |
+
}
|
data/files/A00FT/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A00FT", "accession": "A00FT", "published": true, "md_index": 0, "md_name": "replica 1", "analyses": ["mem-map", "clusters", "clusters-00", "fluctuation", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 7LZP", "DESCRIPTION": "Antigen from Zhao test set, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "[email protected]", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["7LZP"], "FORCED_REFERENCES": null, "REFERENCES": ["P0DPI1"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": 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data/files/A00FU/project.json
ADDED
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| 1 |
+
{
|
| 2 |
+
"accession": "A00FU",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 7M1H",
|
| 6 |
+
"DESCRIPTION": "Antigen from Zhao test set, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
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"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
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|
| 16 |
+
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|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
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"TYPE": "trajectory",
|
| 19 |
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"METHOD": "Classical MD",
|
| 20 |
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|
| 21 |
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"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
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"CITATION": "DynaRepo citation",
|
| 23 |
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"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
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"LINKS": null,
|
| 25 |
+
"PDBIDS": [
|
| 26 |
+
"7M1H"
|
| 27 |
+
],
|
| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P0DPI1"
|
| 31 |
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],
|
| 32 |
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"INPUT_LIGANDS": null,
|
| 33 |
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"LIGANDS": [],
|
| 34 |
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"LIGANDNAMES": null,
|
| 35 |
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"PROTSEQ": [
|
| 36 |
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|
| 37 |
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],
|
| 38 |
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"NUCLSEQ": [],
|
| 39 |
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"DOMAINS": [
|
| 40 |
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"Botulinum neurotoxin type A",
|
| 41 |
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"Botulinum neurotoxin A light chain"
|
| 42 |
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],
|
| 43 |
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"FRAMESTEP": 0.1,
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| 44 |
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|
| 45 |
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"TEMP": 310,
|
| 46 |
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"ENSEMBLE": "NPT",
|
| 47 |
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"FF": [
|
| 48 |
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"CHARMM36m"
|
| 49 |
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|
| 107 |
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| 108 |
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| 128 |
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|
| 129 |
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|
| 130 |
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"pocket_01.pdb",
|
| 131 |
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"pocket_02.pdb",
|
| 132 |
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"pocket_03.pdb",
|
| 133 |
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"pocket_04.pdb",
|
| 134 |
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"pocket_05.pdb",
|
| 135 |
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"pocket_06.pdb",
|
| 136 |
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"pocket_07.pdb",
|
| 137 |
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"pocket_08.pdb",
|
| 138 |
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| 149 |
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| 151 |
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| 152 |
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| 153 |
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data/files/A00FU/records.jsonl
ADDED
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data/files/A00FV/project.json
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| 1 |
+
{
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| 2 |
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"accession": "A00FV",
|
| 3 |
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"published": true,
|
| 4 |
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"metadata": {
|
| 5 |
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"NAME": "Dynarepo 7M3N",
|
| 6 |
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"DESCRIPTION": "Antigen from Zhao test set, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
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"AUTHORS": [
|
| 8 |
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"Omid Mokhtari",
|
| 9 |
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"Hamed Khakzad",
|
| 10 |
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"Yasaman Karami"
|
| 11 |
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],
|
| 12 |
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|
| 13 |
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|
| 14 |
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],
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| 15 |
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"CONTACT": "[email protected]",
|
| 16 |
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"PROGRAM": "GROMACS",
|
| 17 |
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"VERSION": "2024.2",
|
| 18 |
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"TYPE": "trajectory",
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| 19 |
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"METHOD": "Classical MD",
|
| 20 |
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"LICENSE": "Apache License 2.0",
|
| 21 |
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"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
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| 22 |
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| 23 |
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|
| 24 |
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| 25 |
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| 26 |
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"7M3N"
|
| 27 |
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],
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| 28 |
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|
| 29 |
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|
| 30 |
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"P17455"
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| 31 |
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],
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| 32 |
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|
| 33 |
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| 34 |
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| 36 |
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| 37 |
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],
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| 38 |
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| 39 |
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|
| 40 |
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| 41 |
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"Disordered"
|
| 42 |
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],
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| 43 |
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|
| 44 |
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| 45 |
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|
| 46 |
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| 47 |
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|
| 48 |
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"CHARMM36m"
|
| 49 |
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],
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| 50 |
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"WAT": "TIP3P",
|
| 51 |
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| 52 |
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| 53 |
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| 54 |
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| 55 |
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| 56 |
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| 66 |
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| 67 |
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| 69 |
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| 70 |
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| 71 |
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| 74 |
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| 75 |
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| 76 |
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| 77 |
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| 78 |
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| 79 |
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| 80 |
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| 81 |
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| 82 |
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| 83 |
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},
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| 84 |
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| 85 |
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| 86 |
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|
| 87 |
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|
| 88 |
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],
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| 90 |
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| 129 |
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| 130 |
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|
| 131 |
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| 134 |
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| 135 |
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"internalId": "687fa74fc98da4a89753cdb3",
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"creationDate": "2025-07-22T14:59:27.000Z",
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"identifier": "A00FV"
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}
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data/files/A00FW/project.json
ADDED
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@@ -0,0 +1,162 @@
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| 1 |
+
{
|
| 2 |
+
"accession": "A00FW",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 7MPG",
|
| 6 |
+
"DESCRIPTION": "Antigen from Zhao test set, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
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"Hamed Khakzad",
|
| 10 |
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"Yasaman Karami"
|
| 11 |
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],
|
| 12 |
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"GROUPS": [
|
| 13 |
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"Delta team, Inria center at the University of Lorraine"
|
| 14 |
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],
|
| 15 |
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"CONTACT": "[email protected]",
|
| 16 |
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"PROGRAM": "GROMACS",
|
| 17 |
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"VERSION": "2024.2",
|
| 18 |
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"TYPE": "trajectory",
|
| 19 |
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"METHOD": "Classical MD",
|
| 20 |
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"LICENSE": "Apache License 2.0",
|
| 21 |
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"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
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| 22 |
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"CITATION": "DynaRepo citation",
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| 23 |
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"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
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"LINKS": null,
|
| 25 |
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| 26 |
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"7MPG"
|
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],
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"FORCED_REFERENCES": null,
|
| 29 |
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"REFERENCES": [
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| 30 |
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"P03420"
|
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],
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"INPUT_LIGANDS": null,
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"LIGANDS": [],
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"LIGANDNAMES": null,
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"PROTSEQ": [
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| 36 |
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"QNITEEFYQSTCSAVSKGYLSALRTGWYTSVITIELSNIKENKCNGTDAKVKLIKQELDKYKNAVTELQLLMQSTPATNNRAFLGFLLGVGSAIASGVAVCKVLHLEGEVNKIKSALLSTNKAVVSLSNGVSVLTFKVLDLKNYIDKQLLPILNKQSCSISNIETVIEFQQKNNRLLEITREFSVNAGVTTPVSTYMLTNSELLSLINDMPITNDQKKLMSNNVQIVRQQSYSIMCIIKEEVLAYVVQLPLYGVIDTPCWKLHTSPLCTTNTKEGSNICLTRTDRGWYCDNAGSVSFFPQAETCKVQSNRVFCDTMNSLTLPSEVNLCNVDIFNPKYDCKIMTSKTDVSSSVITSLGAIVSCYGKTKCTASNKNRGIIKTFSNGCDYVSNKGVDTVSVGNTLYYVNKQEGKSLYVKGEPIINFYDPLVFPSDEFDASISQVNEKINQSLAFIRKSDELL"
|
| 37 |
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],
|
| 38 |
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"NUCLSEQ": [],
|
| 39 |
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"DOMAINS": [
|
| 40 |
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"Fusion glycoprotein F0",
|
| 41 |
+
"Fusion glycoprotein F2",
|
| 42 |
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"Fusion glycoprotein F1",
|
| 43 |
+
"Fusion peptide",
|
| 44 |
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"Cleavage; by host furin-like protease"
|
| 45 |
+
],
|
| 46 |
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"FRAMESTEP": 0.1,
|
| 47 |
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"TIMESTEP": 2,
|
| 48 |
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"TEMP": 310,
|
| 49 |
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"ENSEMBLE": "NPT",
|
| 50 |
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"FF": [
|
| 51 |
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"CHARMM36m"
|
| 52 |
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],
|
| 53 |
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"WAT": "TIP3P",
|
| 54 |
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"BOXTYPE": "Dodecahedron",
|
| 55 |
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"SYSTATS": 7155,
|
| 56 |
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"SYSTRES": 459,
|
| 57 |
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"PROTATS": 7155,
|
| 58 |
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"PROTRES": 459,
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| 59 |
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"NUCLATS": 0,
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| 60 |
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"NUCLRES": 0,
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"LIPIATS": 0,
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"CARBATS": 0,
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"SOLVATS": 0,
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"COUNCAT": 0,
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"COUNANI": 0,
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"COUNION": 0,
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| 70 |
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"INTERACTIONS": [],
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"PBC_SELECTION": null,
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"CHAINNAMES": null,
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| 74 |
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"CUSTOMS": null,
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| 75 |
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| 76 |
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"PTM": [],
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| 77 |
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"MULTIMERIC": null,
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| 78 |
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"COLLECTIONS": "dynarepo",
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| 79 |
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"WARNINGS": [],
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| 80 |
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"BOXSIZEX": 13.615,
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| 81 |
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"BOXSIZEY": 13.615,
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| 82 |
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"BOXSIZEZ": 9.64326,
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"mdName": "replica 1",
|
| 84 |
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"mdAtoms": 7155,
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| 85 |
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"mdFrames": 5001
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| 86 |
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},
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| 87 |
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"mds": [
|
| 88 |
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"replica 1",
|
| 89 |
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"replica 2",
|
| 90 |
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"replica 3"
|
| 91 |
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],
|
| 92 |
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"mdref": 0,
|
| 93 |
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"files": [
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| 95 |
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| 97 |
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| 98 |
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| 99 |
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| 100 |
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| 101 |
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| 102 |
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| 103 |
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| 104 |
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| 105 |
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| 106 |
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| 107 |
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"pca_trajectory_11.bin",
|
| 108 |
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"structure.pdb",
|
| 109 |
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"trajectory.xtc",
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| 110 |
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"clusters_00_screenshot_00.jpg",
|
| 111 |
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"clusters_00_screenshot_01.jpg",
|
| 112 |
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| 113 |
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"clusters_00_screenshot_03.jpg",
|
| 114 |
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|
| 115 |
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"clusters_00_screenshot_05.jpg",
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| 116 |
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"clusters_00_screenshot_06.jpg",
|
| 117 |
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"clusters_00_screenshot_07.jpg",
|
| 118 |
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|
| 119 |
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|
| 120 |
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"clusters_00_screenshot_10.jpg",
|
| 121 |
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"clusters_00_screenshot_11.jpg",
|
| 122 |
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"clusters_00_screenshot_12.jpg",
|
| 123 |
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"clusters_00_screenshot_13.jpg",
|
| 124 |
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"clusters_00_screenshot_14.jpg",
|
| 125 |
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|
| 126 |
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"clusters_00_screenshot_16.jpg",
|
| 127 |
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"clusters_00_screenshot_17.jpg",
|
| 128 |
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"clusters_00_screenshot_18.jpg",
|
| 129 |
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"clusters_00_screenshot_19.jpg",
|
| 130 |
+
"pocket_01.pdb",
|
| 131 |
+
"pocket_02.pdb",
|
| 132 |
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"pocket_03.pdb",
|
| 133 |
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"pocket_04.pdb",
|
| 134 |
+
"pocket_05.pdb",
|
| 135 |
+
"pocket_06.pdb",
|
| 136 |
+
"pocket_07.pdb",
|
| 137 |
+
"pocket_08.pdb",
|
| 138 |
+
"pocket_09.pdb"
|
| 139 |
+
],
|
| 140 |
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"analyses": [
|
| 141 |
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"mem-map",
|
| 142 |
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"clusters",
|
| 143 |
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"clusters-00",
|
| 144 |
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"fluctuation",
|
| 145 |
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"pca",
|
| 146 |
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"pockets",
|
| 147 |
+
"rgyr",
|
| 148 |
+
"rmsd-pairwise",
|
| 149 |
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"rmsd-perres",
|
| 150 |
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"rmsds",
|
| 151 |
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"sasa",
|
| 152 |
+
"tmscores"
|
| 153 |
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],
|
| 154 |
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"updateDate": "2025-07-23T12:43:00.351Z",
|
| 155 |
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"mdcount": 3,
|
| 156 |
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|
| 157 |
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|
| 158 |
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|
| 159 |
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"internalId": "687fa89d203e086de9020ae1",
|
| 160 |
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"creationDate": "2025-07-22T15:05:01.000Z",
|
| 161 |
+
"identifier": "A00FW"
|
| 162 |
+
}
|
data/files/A00FW/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A00FW", "accession": "A00FW", "published": true, "md_index": 0, "md_name": "replica 1", "analyses": ["mem-map", "clusters", "clusters-00", "fluctuation", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 7MPG", "DESCRIPTION": "Antigen from Zhao test set, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "[email protected]", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["7MPG"], "FORCED_REFERENCES": null, "REFERENCES": ["P03420"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": 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|
| 3 |
+
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data/files/A00FX/project.json
ADDED
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| 1 |
+
{
|
| 2 |
+
"accession": "A00FX",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 7MZJ",
|
| 6 |
+
"DESCRIPTION": "Antigen from Zhao test set, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"CONTACT": "[email protected]",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
+
"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
+
"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
+
"CITATION": "DynaRepo citation",
|
| 23 |
+
"THANKS": "DynaRepo Acknowledgements",
|
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data/files/A00FX/records.jsonl
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data/files/A00FY/project.json
ADDED
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@@ -0,0 +1,169 @@
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| 1 |
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{
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| 2 |
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"accession": "A00FY",
|
| 3 |
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"published": true,
|
| 4 |
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"metadata": {
|
| 5 |
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"NAME": "Dynarepo 7MZK",
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| 6 |
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|
| 7 |
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|
| 8 |
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"Omid Mokhtari",
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| 9 |
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"Hamed Khakzad",
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],
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"Spike glycoprotein",
|
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| 42 |
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"BetaCoV S1-CTD",
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| 43 |
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"Disordered",
|
| 44 |
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"Receptor-binding domain (RBD)",
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| 45 |
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"Integrin-binding motif;",
|
| 46 |
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"Receptor-binding motif; binding to human ACE2",
|
| 47 |
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"Immunodominant HLA epitope recognized by the CD8+; called NF9 peptide"
|
| 48 |
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],
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| 49 |
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"FRAMESTEP": 0.1,
|
| 50 |
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| 51 |
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"TEMP": 310,
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| 52 |
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"ENSEMBLE": "NPT",
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| 53 |
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"FF": [
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| 54 |
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"CHARMM36m"
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| 55 |
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],
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| 56 |
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"WAT": "TIP3P",
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"BOXTYPE": "Dodecahedron",
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},
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|
| 92 |
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| 95 |
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"files": [
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| 104 |
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| 105 |
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| 106 |
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| 124 |
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| 125 |
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| 126 |
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|
| 127 |
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|
| 128 |
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|
| 129 |
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|
| 130 |
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|
| 131 |
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| 132 |
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|
| 133 |
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|
| 134 |
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|
| 135 |
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| 136 |
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|
| 137 |
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| 138 |
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|
| 139 |
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|
| 140 |
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|
| 141 |
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"pocket_01.pdb",
|
| 142 |
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"pocket_02.pdb",
|
| 143 |
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"pocket_03.pdb",
|
| 144 |
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"pocket_04.pdb",
|
| 145 |
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"pocket_05.pdb"
|
| 146 |
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],
|
| 147 |
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"analyses": [
|
| 148 |
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"mem-map",
|
| 149 |
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"clusters",
|
| 150 |
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"clusters-00",
|
| 151 |
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"fluctuation",
|
| 152 |
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"pca",
|
| 153 |
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"pockets",
|
| 154 |
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"rgyr",
|
| 155 |
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|
| 156 |
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|
| 157 |
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"rmsds",
|
| 158 |
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"sasa",
|
| 159 |
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"tmscores"
|
| 160 |
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],
|
| 161 |
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"updateDate": "2025-07-23T12:43:06.192Z",
|
| 162 |
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"mdcount": 3,
|
| 163 |
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| 164 |
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| 166 |
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"internalId": "687faa3217444263e275a7f9",
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| 167 |
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"creationDate": "2025-07-22T15:11:46.000Z",
|
| 168 |
+
"identifier": "A00FY"
|
| 169 |
+
}
|
data/files/A00FY/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
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data/files/A00FZ/project.json
ADDED
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| 1 |
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{
|
| 2 |
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"accession": "A00FZ",
|
| 3 |
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"published": true,
|
| 4 |
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"metadata": {
|
| 5 |
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"NAME": "Dynarepo 7MZM",
|
| 6 |
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"DESCRIPTION": "Antigen from Zhao test set, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
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"AUTHORS": [
|
| 8 |
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"Omid Mokhtari",
|
| 9 |
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"Hamed Khakzad",
|
| 10 |
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"Yasaman Karami"
|
| 11 |
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| 12 |
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| 13 |
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|
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"TYPE": "trajectory",
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"METHOD": "Classical MD",
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"LICENSE": "Apache License 2.0",
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| 36 |
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|
| 37 |
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],
|
| 38 |
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"NUCLSEQ": [],
|
| 39 |
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"DOMAINS": [
|
| 40 |
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"Spike glycoprotein",
|
| 41 |
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"Spike protein S1",
|
| 42 |
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"BetaCoV S1-CTD",
|
| 43 |
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"Disordered",
|
| 44 |
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"Receptor-binding domain (RBD)",
|
| 45 |
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"Integrin-binding motif;",
|
| 46 |
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"Receptor-binding motif; binding to human ACE2",
|
| 47 |
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"Immunodominant HLA epitope recognized by the CD8+; called NF9 peptide"
|
| 48 |
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],
|
| 49 |
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"FRAMESTEP": 0.1,
|
| 50 |
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"TIMESTEP": 2,
|
| 51 |
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"TEMP": 310,
|
| 52 |
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"ENSEMBLE": "NPT",
|
| 53 |
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"FF": [
|
| 54 |
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"CHARMM36m"
|
| 55 |
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],
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| 56 |
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"WAT": "TIP3P",
|
| 57 |
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"BOXTYPE": "Dodecahedron",
|
| 58 |
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"SYSTATS": 2972,
|
| 59 |
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"SYSTRES": 192,
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| 60 |
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| 89 |
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},
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| 91 |
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| 92 |
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| 93 |
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|
| 94 |
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| 95 |
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| 111 |
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| 112 |
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| 113 |
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| 115 |
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| 116 |
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| 124 |
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|
| 125 |
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| 126 |
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|
| 127 |
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|
| 128 |
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|
| 129 |
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| 130 |
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| 131 |
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| 132 |
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| 133 |
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| 134 |
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"clusters_00_screenshot_14.jpg",
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| 135 |
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|
| 136 |
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| 137 |
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"clusters_00_screenshot_17.jpg",
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| 138 |
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|
| 139 |
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"clusters_00_screenshot_19.jpg",
|
| 140 |
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"pocket_01.pdb",
|
| 141 |
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"pocket_02.pdb"
|
| 142 |
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],
|
| 143 |
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"analyses": [
|
| 144 |
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"mem-map",
|
| 145 |
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"clusters",
|
| 146 |
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"clusters-00",
|
| 147 |
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"fluctuation",
|
| 148 |
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|
| 149 |
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|
| 150 |
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|
| 151 |
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|
| 152 |
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|
| 153 |
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"rmsds",
|
| 154 |
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|
| 155 |
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"tmscores"
|
| 156 |
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],
|
| 157 |
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"updateDate": "2025-07-23T12:43:09.509Z",
|
| 158 |
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"mdcount": 3,
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| 159 |
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| 161 |
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| 162 |
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| 163 |
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"creationDate": "2025-07-22T15:13:56.000Z",
|
| 164 |
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"identifier": "A00FZ"
|
| 165 |
+
}
|
data/files/A00FZ/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A00FZ", "accession": "A00FZ", "published": true, "md_index": 0, "md_name": "replica 1", "analyses": ["mem-map", "clusters", "clusters-00", "fluctuation", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 7MZM", "DESCRIPTION": "Antigen from Zhao test set, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "[email protected]", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["7MZM"], "FORCED_REFERENCES": null, "REFERENCES": ["P0DTC2"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": 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|
| 3 |
+
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data/files/A00G0/project.json
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| 1 |
+
{
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| 2 |
+
"accession": "A00G0",
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| 3 |
+
"published": true,
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| 4 |
+
"metadata": {
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| 5 |
+
"NAME": "Dynarepo 7N4J",
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| 6 |
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"DESCRIPTION": "Antigen from Zhao test set, Classical MD simulations, 3 replicates of 500 ns",
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| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
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"Hamed Khakzad",
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| 10 |
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"Yasaman Karami"
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| 11 |
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],
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| 12 |
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| 14 |
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"TYPE": "trajectory",
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"METHOD": "Classical MD",
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"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
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"CITATION": "DynaRepo citation",
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"THANKS": "DynaRepo Acknowledgements",
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"7N4J"
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"P0DTC2"
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| 36 |
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"NITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPGSHHH"
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| 37 |
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],
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"NUCLSEQ": [],
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| 39 |
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"DOMAINS": [
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| 40 |
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"Spike glycoprotein",
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"Spike protein S1",
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"BetaCoV S1-CTD",
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| 43 |
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"Disordered",
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"Receptor-binding domain (RBD)",
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| 45 |
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"Integrin-binding motif;",
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"Receptor-binding motif; binding to human ACE2",
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| 47 |
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"Immunodominant HLA epitope recognized by the CD8+; called NF9 peptide"
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| 48 |
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],
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"CHARMM36m"
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| 91 |
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"replica 1",
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"replica 3"
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| 103 |
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| 107 |
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| 108 |
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"pca_trajectory_09.bin",
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| 109 |
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"clusters_00_screenshot_05.jpg",
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| 123 |
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"clusters_00_screenshot_06.jpg",
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| 124 |
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"clusters_00_screenshot_15.jpg",
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| 133 |
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"clusters_00_screenshot_16.jpg",
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| 134 |
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"clusters_00_screenshot_17.jpg",
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| 135 |
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"clusters_00_screenshot_18.jpg",
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| 136 |
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"clusters_00_screenshot_19.jpg",
|
| 137 |
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"pocket_01.pdb",
|
| 138 |
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"pocket_02.pdb",
|
| 139 |
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"pocket_03.pdb",
|
| 140 |
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"pocket_04.pdb"
|
| 141 |
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],
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| 142 |
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"analyses": [
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| 143 |
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"mem-map",
|
| 144 |
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"clusters",
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| 145 |
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| 146 |
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"fluctuation",
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| 147 |
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"pca",
|
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"pockets",
|
| 149 |
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"rgyr",
|
| 150 |
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"rmsd-pairwise",
|
| 151 |
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"rmsd-perres",
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| 152 |
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"rmsds",
|
| 153 |
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"sasa",
|
| 154 |
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"tmscores"
|
| 155 |
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],
|
| 156 |
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"updateDate": "2025-07-23T12:43:23.459Z",
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| 157 |
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"mdcount": 3,
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| 158 |
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"creationDate": "2025-07-22T15:16:09.000Z",
|
| 163 |
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"identifier": "A00G0"
|
| 164 |
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}
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data/files/A00G0/records.jsonl
ADDED
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| 3 |
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data/files/A00G1/project.json
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| 1 |
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{
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| 2 |
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| 3 |
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| 4 |
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"metadata": {
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| 5 |
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|
| 6 |
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|
| 7 |
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|
| 8 |
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"Omid Mokhtari",
|
| 9 |
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| 10 |
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| 11 |
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| 17 |
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| 18 |
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| 19 |
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| 20 |
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| 41 |
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| 42 |
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| 45 |
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| 46 |
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| 47 |
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| 48 |
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| 49 |
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| 86 |
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|
| 135 |
+
"pocket_09.pdb",
|
| 136 |
+
"pocket_10.pdb"
|
| 137 |
+
],
|
| 138 |
+
"analyses": [
|
| 139 |
+
"mem-map",
|
| 140 |
+
"clusters",
|
| 141 |
+
"clusters-00",
|
| 142 |
+
"fluctuation",
|
| 143 |
+
"pca",
|
| 144 |
+
"pockets",
|
| 145 |
+
"rgyr",
|
| 146 |
+
"rmsd-pairwise",
|
| 147 |
+
"rmsd-perres",
|
| 148 |
+
"rmsds",
|
| 149 |
+
"sasa",
|
| 150 |
+
"tmscores"
|
| 151 |
+
],
|
| 152 |
+
"updateDate": "2025-07-23T12:43:26.130Z",
|
| 153 |
+
"mdcount": 3,
|
| 154 |
+
"mdIndex": 0,
|
| 155 |
+
"mdNumber": 1,
|
| 156 |
+
"refframe": 0,
|
| 157 |
+
"internalId": "687fabbc30e50482932f1b47",
|
| 158 |
+
"creationDate": "2025-07-22T15:18:20.000Z",
|
| 159 |
+
"identifier": "A00G1"
|
| 160 |
+
}
|
data/files/A00G1/records.jsonl
ADDED
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@@ -0,0 +1,3 @@
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| 1 |
+
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data/files/A00G2/project.json
ADDED
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@@ -0,0 +1,161 @@
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| 1 |
+
{
|
| 2 |
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"accession": "A00G2",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
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"NAME": "Dynarepo 7NFQ",
|
| 6 |
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"DESCRIPTION": "Antigen from Zhao test set, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
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"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
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"Hamed Khakzad",
|
| 10 |
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"Yasaman Karami"
|
| 11 |
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],
|
| 12 |
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"GROUPS": [
|
| 13 |
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"Delta team, Inria center at the University of Lorraine"
|
| 14 |
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],
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| 15 |
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"CONTACT": "[email protected]",
|
| 16 |
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"PROGRAM": "GROMACS",
|
| 17 |
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"VERSION": "2024.2",
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| 18 |
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"TYPE": "trajectory",
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| 19 |
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"METHOD": "Classical MD",
|
| 20 |
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"LICENSE": "Apache License 2.0",
|
| 21 |
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"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
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"CITATION": "DynaRepo citation",
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| 24 |
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"7NFQ"
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],
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| 35 |
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| 36 |
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|
| 37 |
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],
|
| 38 |
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"NUCLSEQ": [],
|
| 39 |
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"DOMAINS": [
|
| 40 |
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"Polymerase basic protein 2 helical",
|
| 41 |
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"Influenza RNA polymerase PB2 CAP binding",
|
| 42 |
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"Influenza RNA polymerase PB2 sixth"
|
| 43 |
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],
|
| 44 |
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"FRAMESTEP": 0.1,
|
| 45 |
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"TIMESTEP": 2,
|
| 46 |
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"TEMP": 310,
|
| 47 |
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"ENSEMBLE": "NPT",
|
| 48 |
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"FF": [
|
| 49 |
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"CHARMM36m"
|
| 50 |
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],
|
| 51 |
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"WAT": "TIP3P",
|
| 52 |
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"BOXTYPE": "Dodecahedron",
|
| 53 |
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"SYSTATS": 4479,
|
| 54 |
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"SYSTRES": 282,
|
| 55 |
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"PROTATS": 4479,
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| 56 |
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"PROTRES": 282,
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"NUCLATS": 0,
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"COUNION": 0,
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"INTERACTIONS": [],
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"PBC_SELECTION": null,
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"CHAINNAMES": null,
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"MEMBRANES": null,
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"PTM": [],
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| 75 |
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"MULTIMERIC": null,
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| 76 |
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"COLLECTIONS": "dynarepo",
|
| 77 |
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"WARNINGS": [],
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| 78 |
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| 79 |
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"BOXSIZEY": 8.63735,
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"BOXSIZEZ": 6.07308,
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| 84 |
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},
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| 85 |
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"mds": [
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| 86 |
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"replica 1",
|
| 87 |
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"replica 2",
|
| 88 |
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"replica 3"
|
| 89 |
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],
|
| 90 |
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"mdref": 0,
|
| 91 |
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"files": [
|
| 92 |
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"topology.tpr",
|
| 93 |
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"screenshot.jpg",
|
| 94 |
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"trajectory.bin",
|
| 95 |
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"pca_trajectory_01.bin",
|
| 96 |
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|
| 97 |
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|
| 98 |
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|
| 99 |
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| 100 |
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|
| 101 |
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| 102 |
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| 103 |
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| 104 |
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| 105 |
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| 106 |
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|
| 107 |
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|
| 108 |
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"structure.pdb",
|
| 109 |
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"trajectory.xtc",
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| 110 |
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|
| 111 |
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"clusters_00_screenshot_01.jpg",
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| 112 |
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| 113 |
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| 114 |
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| 115 |
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| 116 |
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| 117 |
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| 118 |
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| 119 |
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"clusters_00_screenshot_09.jpg",
|
| 120 |
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"clusters_00_screenshot_10.jpg",
|
| 121 |
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|
| 122 |
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|
| 123 |
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"clusters_00_screenshot_13.jpg",
|
| 124 |
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"clusters_00_screenshot_14.jpg",
|
| 125 |
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"clusters_00_screenshot_15.jpg",
|
| 126 |
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"clusters_00_screenshot_16.jpg",
|
| 127 |
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"clusters_00_screenshot_17.jpg",
|
| 128 |
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"clusters_00_screenshot_18.jpg",
|
| 129 |
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"clusters_00_screenshot_19.jpg",
|
| 130 |
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"pocket_01.pdb",
|
| 131 |
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"pocket_02.pdb",
|
| 132 |
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"pocket_03.pdb",
|
| 133 |
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"pocket_04.pdb",
|
| 134 |
+
"pocket_05.pdb",
|
| 135 |
+
"pocket_06.pdb",
|
| 136 |
+
"pocket_07.pdb",
|
| 137 |
+
"pocket_08.pdb"
|
| 138 |
+
],
|
| 139 |
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"analyses": [
|
| 140 |
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"mem-map",
|
| 141 |
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"clusters",
|
| 142 |
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"clusters-00",
|
| 143 |
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"fluctuation",
|
| 144 |
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"pca",
|
| 145 |
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"pockets",
|
| 146 |
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"rgyr",
|
| 147 |
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"rmsd-pairwise",
|
| 148 |
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"rmsd-perres",
|
| 149 |
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"rmsds",
|
| 150 |
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"sasa",
|
| 151 |
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"tmscores"
|
| 152 |
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],
|
| 153 |
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"updateDate": "2025-07-23T12:43:29.211Z",
|
| 154 |
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"mdcount": 3,
|
| 155 |
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| 156 |
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|
| 157 |
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| 158 |
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"internalId": "687face6a24f4d7086429c51",
|
| 159 |
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"creationDate": "2025-07-22T15:23:18.000Z",
|
| 160 |
+
"identifier": "A00G2"
|
| 161 |
+
}
|
data/files/A00G2/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A00G2", "accession": "A00G2", "published": true, "md_index": 0, "md_name": "replica 1", "analyses": ["mem-map", "clusters", "clusters-00", "fluctuation", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 7NFQ", "DESCRIPTION": "Antigen from Zhao test set, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "[email protected]", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["7NFQ"], "FORCED_REFERENCES": null, "REFERENCES": ["Q6E3N3"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": 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|
| 3 |
+
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data/files/A00G3/project.json
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{
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"accession": "A00G3",
|
| 3 |
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"published": true,
|
| 4 |
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"metadata": {
|
| 5 |
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"NAME": "Dynarepo 7NFR",
|
| 6 |
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|
| 7 |
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|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
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"Hamed Khakzad",
|
| 10 |
+
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|
| 11 |
+
],
|
| 12 |
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|
| 13 |
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|
| 14 |
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|
| 15 |
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|
| 16 |
+
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|
| 17 |
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|
| 18 |
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|
| 19 |
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|
| 20 |
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|
| 21 |
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|
| 22 |
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|
| 23 |
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|
| 24 |
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|
| 25 |
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|
| 26 |
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|
| 27 |
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|
| 28 |
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|
| 29 |
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"REFERENCES": [
|
| 30 |
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|
| 31 |
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|
| 32 |
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|
| 33 |
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"LIGANDS": [],
|
| 34 |
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|
| 35 |
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|
| 36 |
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|
| 37 |
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],
|
| 38 |
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|
| 39 |
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"DOMAINS": [
|
| 40 |
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"Polymerase basic protein 2 helical",
|
| 41 |
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"Influenza RNA polymerase PB2 CAP binding",
|
| 42 |
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"Influenza RNA polymerase PB2 sixth"
|
| 43 |
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],
|
| 44 |
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|
| 45 |
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|
| 46 |
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"TEMP": 310,
|
| 47 |
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|
| 48 |
+
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|
| 49 |
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"CHARMM36m"
|
| 50 |
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|
| 51 |
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|
| 52 |
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|
| 53 |
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|
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| 55 |
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| 56 |
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|
| 67 |
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|
| 68 |
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|
| 69 |
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|
| 70 |
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|
| 71 |
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|
| 72 |
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|
| 73 |
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|
| 74 |
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|
| 75 |
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|
| 76 |
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"COLLECTIONS": "dynarepo",
|
| 77 |
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|
| 78 |
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|
| 79 |
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|
| 80 |
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|
| 81 |
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|
| 82 |
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|
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|
| 84 |
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},
|
| 85 |
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"mds": [
|
| 86 |
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"replica 1",
|
| 87 |
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"replica 2",
|
| 88 |
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"replica 3"
|
| 89 |
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],
|
| 90 |
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"mdref": 0,
|
| 91 |
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"files": [
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| 92 |
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| 93 |
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| 94 |
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|
| 95 |
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"pca_trajectory_01.bin",
|
| 96 |
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"pca_trajectory_02.bin",
|
| 97 |
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"pca_trajectory_03.bin",
|
| 98 |
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"pca_trajectory_04.bin",
|
| 99 |
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"pca_trajectory_05.bin",
|
| 100 |
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"pca_trajectory_06.bin",
|
| 101 |
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"structure.pdb",
|
| 102 |
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"trajectory.xtc",
|
| 103 |
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"clusters_00_screenshot_00.jpg",
|
| 104 |
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"clusters_00_screenshot_01.jpg",
|
| 105 |
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"clusters_00_screenshot_02.jpg",
|
| 106 |
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"clusters_00_screenshot_03.jpg",
|
| 107 |
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"clusters_00_screenshot_04.jpg",
|
| 108 |
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"clusters_00_screenshot_05.jpg",
|
| 109 |
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"clusters_00_screenshot_06.jpg",
|
| 110 |
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"clusters_00_screenshot_07.jpg",
|
| 111 |
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"clusters_00_screenshot_08.jpg",
|
| 112 |
+
"clusters_00_screenshot_09.jpg",
|
| 113 |
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"clusters_00_screenshot_10.jpg",
|
| 114 |
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"clusters_00_screenshot_11.jpg",
|
| 115 |
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"clusters_00_screenshot_12.jpg",
|
| 116 |
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"clusters_00_screenshot_13.jpg",
|
| 117 |
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"clusters_00_screenshot_14.jpg",
|
| 118 |
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"clusters_00_screenshot_15.jpg",
|
| 119 |
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"clusters_00_screenshot_16.jpg",
|
| 120 |
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"clusters_00_screenshot_17.jpg",
|
| 121 |
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"clusters_00_screenshot_18.jpg",
|
| 122 |
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"clusters_00_screenshot_19.jpg",
|
| 123 |
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"clusters_00_screenshot_20.jpg",
|
| 124 |
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"clusters_00_screenshot_21.jpg",
|
| 125 |
+
"pocket_01.pdb",
|
| 126 |
+
"pocket_02.pdb",
|
| 127 |
+
"pocket_03.pdb",
|
| 128 |
+
"pocket_04.pdb",
|
| 129 |
+
"pocket_05.pdb",
|
| 130 |
+
"pocket_06.pdb",
|
| 131 |
+
"pocket_07.pdb"
|
| 132 |
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],
|
| 133 |
+
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|
| 134 |
+
"mem-map",
|
| 135 |
+
"clusters",
|
| 136 |
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"clusters-00",
|
| 137 |
+
"fluctuation",
|
| 138 |
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"pca",
|
| 139 |
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"pockets",
|
| 140 |
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"rgyr",
|
| 141 |
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"rmsd-pairwise",
|
| 142 |
+
"rmsd-perres",
|
| 143 |
+
"rmsds",
|
| 144 |
+
"sasa",
|
| 145 |
+
"tmscores"
|
| 146 |
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|
| 147 |
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|
| 148 |
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| 149 |
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| 153 |
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|
| 154 |
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"identifier": "A00G3"
|
| 155 |
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}
|
data/files/A00G3/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
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data/files/A00G4/project.json
ADDED
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| 1 |
+
{
|
| 2 |
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"accession": "A00G4",
|
| 3 |
+
"published": true,
|
| 4 |
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"metadata": {
|
| 5 |
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"NAME": "Dynarepo 7NP1",
|
| 6 |
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"DESCRIPTION": "Antigen from Zhao test set, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
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"Hamed Khakzad",
|
| 10 |
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"Yasaman Karami"
|
| 11 |
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],
|
| 12 |
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"GROUPS": [
|
| 13 |
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"Delta team, Inria center at the University of Lorraine"
|
| 14 |
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],
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| 15 |
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"CONTACT": "[email protected]",
|
| 16 |
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"PROGRAM": "GROMACS",
|
| 17 |
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"VERSION": "2024.2",
|
| 18 |
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"TYPE": "trajectory",
|
| 19 |
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"METHOD": "Classical MD",
|
| 20 |
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"LICENSE": "Apache License 2.0",
|
| 21 |
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"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
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"CITATION": "DynaRepo citation",
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|
| 24 |
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|
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"7NP1"
|
| 27 |
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|
| 29 |
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"REFERENCES": [
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| 30 |
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"P0DTC2"
|
| 31 |
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],
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| 32 |
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"INPUT_LIGANDS": null,
|
| 33 |
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"LIGANDS": [],
|
| 34 |
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"LIGANDNAMES": null,
|
| 35 |
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"PROTSEQ": [
|
| 36 |
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|
| 37 |
+
],
|
| 38 |
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"NUCLSEQ": [],
|
| 39 |
+
"DOMAINS": [
|
| 40 |
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"Spike glycoprotein",
|
| 41 |
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"Spike protein S1",
|
| 42 |
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"BetaCoV S1-CTD",
|
| 43 |
+
"Disordered",
|
| 44 |
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"Receptor-binding domain (RBD)",
|
| 45 |
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"Integrin-binding motif;",
|
| 46 |
+
"Receptor-binding motif; binding to human ACE2",
|
| 47 |
+
"Immunodominant HLA epitope recognized by the CD8+; called NF9 peptide"
|
| 48 |
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],
|
| 49 |
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"FRAMESTEP": 0.1,
|
| 50 |
+
"TIMESTEP": 2,
|
| 51 |
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"TEMP": 310,
|
| 52 |
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"ENSEMBLE": "NPT",
|
| 53 |
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"FF": [
|
| 54 |
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"CHARMM36m"
|
| 55 |
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],
|
| 56 |
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"WAT": "TIP3P",
|
| 57 |
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"BOXTYPE": "Dodecahedron",
|
| 58 |
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"SYSTATS": 2788,
|
| 59 |
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"SYSTRES": 179,
|
| 60 |
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"PROTATS": 2788,
|
| 61 |
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| 62 |
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"NUCLATS": 0,
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| 63 |
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"NUCLRES": 0,
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"CARBRES": 0,
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"COUNANI": 0,
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| 72 |
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| 79 |
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"PTM": [],
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| 80 |
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"MULTIMERIC": null,
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| 81 |
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"COLLECTIONS": "dynarepo",
|
| 82 |
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"WARNINGS": [],
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| 83 |
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"BOXSIZEX": 9.00091,
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| 84 |
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"BOXSIZEY": 9.00091,
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| 85 |
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"BOXSIZEZ": 6.41783,
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"mdName": "replica 1",
|
| 87 |
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"mdAtoms": 2788,
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| 88 |
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"mdFrames": 5001
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| 89 |
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},
|
| 90 |
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"mds": [
|
| 91 |
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"replica 1",
|
| 92 |
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"replica 2",
|
| 93 |
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"replica 3"
|
| 94 |
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],
|
| 95 |
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"mdref": 0,
|
| 96 |
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"files": [
|
| 97 |
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|
| 98 |
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|
| 99 |
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"trajectory.bin",
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| 100 |
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|
| 101 |
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| 102 |
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|
| 103 |
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|
| 104 |
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|
| 105 |
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| 106 |
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|
| 107 |
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|
| 108 |
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| 109 |
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| 110 |
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|
| 111 |
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"pca_trajectory_12.bin",
|
| 112 |
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"structure.pdb",
|
| 113 |
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"trajectory.xtc",
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| 114 |
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"clusters_00_screenshot_00.jpg",
|
| 115 |
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"clusters_00_screenshot_01.jpg",
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| 116 |
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"clusters_00_screenshot_02.jpg",
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| 117 |
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"clusters_00_screenshot_03.jpg",
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| 118 |
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"clusters_00_screenshot_04.jpg",
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| 119 |
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"clusters_00_screenshot_05.jpg",
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| 120 |
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"clusters_00_screenshot_06.jpg",
|
| 121 |
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"clusters_00_screenshot_07.jpg",
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| 122 |
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"clusters_00_screenshot_08.jpg",
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| 123 |
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| 124 |
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"clusters_00_screenshot_10.jpg",
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| 125 |
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| 126 |
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|
| 127 |
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|
| 128 |
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|
| 129 |
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|
| 130 |
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|
| 131 |
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|
| 132 |
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"clusters_00_screenshot_18.jpg",
|
| 133 |
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"pocket_01.pdb",
|
| 134 |
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"pocket_02.pdb"
|
| 135 |
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],
|
| 136 |
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"analyses": [
|
| 137 |
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"mem-map",
|
| 138 |
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"clusters",
|
| 139 |
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"clusters-00",
|
| 140 |
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"fluctuation",
|
| 141 |
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"pca",
|
| 142 |
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"pockets",
|
| 143 |
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"rgyr",
|
| 144 |
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"rmsd-pairwise",
|
| 145 |
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"rmsd-perres",
|
| 146 |
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"rmsds",
|
| 147 |
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"sasa",
|
| 148 |
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"tmscores"
|
| 149 |
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],
|
| 150 |
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"updateDate": "2025-07-23T12:43:34.809Z",
|
| 151 |
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"mdcount": 3,
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| 152 |
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| 154 |
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| 155 |
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"internalId": "687fae5e12aac62002154663",
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| 156 |
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"creationDate": "2025-07-22T15:29:34.000Z",
|
| 157 |
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"identifier": "A00G4"
|
| 158 |
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}
|
data/files/A00G4/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A00G4", "accession": "A00G4", "published": true, "md_index": 0, "md_name": "replica 1", "analyses": ["mem-map", "clusters", "clusters-00", "fluctuation", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 7NP1", "DESCRIPTION": "Antigen from Zhao test set, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "[email protected]", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["7NP1"], "FORCED_REFERENCES": null, "REFERENCES": ["P0DTC2"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": 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data/files/A00G5/project.json
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| 1 |
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{
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| 3 |
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| 4 |
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| 5 |
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| 6 |
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| 7 |
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| 8 |
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| 9 |
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| 11 |
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|
| 111 |
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"clusters_00_screenshot_02.jpg",
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"clusters_00_screenshot_03.jpg",
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"clusters_00_screenshot_04.jpg",
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"clusters_00_screenshot_05.jpg",
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"clusters_00_screenshot_06.jpg",
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"clusters_00_screenshot_07.jpg",
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"clusters_00_screenshot_08.jpg",
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"clusters_00_screenshot_13.jpg",
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"clusters_00_screenshot_14.jpg",
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"clusters_00_screenshot_15.jpg",
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"clusters_00_screenshot_16.jpg",
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"clusters_00_screenshot_17.jpg",
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"clusters_00_screenshot_18.jpg",
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"clusters_00_screenshot_19.jpg",
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+
"clusters_00_screenshot_20.jpg",
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| 130 |
+
"clusters_00_screenshot_21.jpg",
|
| 131 |
+
"pocket_01.pdb",
|
| 132 |
+
"pocket_02.pdb",
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| 133 |
+
"pocket_03.pdb",
|
| 134 |
+
"pocket_04.pdb",
|
| 135 |
+
"pocket_05.pdb",
|
| 136 |
+
"pocket_06.pdb"
|
| 137 |
+
],
|
| 138 |
+
"analyses": [
|
| 139 |
+
"mem-map",
|
| 140 |
+
"clusters",
|
| 141 |
+
"clusters-00",
|
| 142 |
+
"fluctuation",
|
| 143 |
+
"pca",
|
| 144 |
+
"pockets",
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| 145 |
+
"rgyr",
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| 146 |
+
"rmsd-pairwise",
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| 147 |
+
"rmsd-perres",
|
| 148 |
+
"rmsds",
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| 149 |
+
"sasa",
|
| 150 |
+
"tmscores"
|
| 151 |
+
],
|
| 152 |
+
"updateDate": "2025-07-23T12:43:37.595Z",
|
| 153 |
+
"mdcount": 3,
|
| 154 |
+
"mdIndex": 0,
|
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+
"mdNumber": 1,
|
| 156 |
+
"refframe": 0,
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+
"internalId": "687faecec8b75651103c532e",
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| 158 |
+
"creationDate": "2025-07-22T15:31:26.000Z",
|
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+
"identifier": "A00G5"
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+
}
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data/files/A00G5/records.jsonl
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data/files/A00G6/project.json
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| 1 |
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{
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| 2 |
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|
| 3 |
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|
| 4 |
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|
| 5 |
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|
| 6 |
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|
| 7 |
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|
| 8 |
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|
| 9 |
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|
| 10 |
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| 11 |
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| 40 |
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| 47 |
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| 49 |
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| 127 |
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| 128 |
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| 129 |
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| 131 |
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|
| 132 |
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"pocket_01.pdb",
|
| 133 |
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| 134 |
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|
| 135 |
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|
| 136 |
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|
| 137 |
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|
| 138 |
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|
| 139 |
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|
| 140 |
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|
| 141 |
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|
| 142 |
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],
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| 143 |
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|
| 144 |
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|
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| 146 |
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|
| 150 |
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|
| 151 |
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],
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"updateDate": "2025-07-23T12:43:40.339Z",
|
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"creationDate": "2025-07-22T15:34:21.000Z",
|
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|
| 165 |
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|
data/files/A00G6/records.jsonl
ADDED
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@@ -0,0 +1,3 @@
|
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|
|
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|
|
|
|
|
|
|
|
| 1 |
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{"project_identifier": "A00G6", "accession": "A00G6", "published": true, "md_index": 0, "md_name": "replica 1", "analyses": ["mem-map", "clusters", "clusters-00", "fluctuation", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 7NX3", "DESCRIPTION": "Antigen from Zhao test set, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "[email protected]", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["7NX3"], "FORCED_REFERENCES": null, "REFERENCES": ["Q9UM73"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": 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data/files/A00G7/project.json
ADDED
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| 1 |
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{
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| 2 |
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"accession": "A00G7",
|
| 3 |
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"published": true,
|
| 4 |
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"metadata": {
|
| 5 |
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"NAME": "Dynarepo 7OM4",
|
| 6 |
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|
| 7 |
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"AUTHORS": [
|
| 8 |
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"Omid Mokhtari",
|
| 9 |
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"Hamed Khakzad",
|
| 10 |
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|
| 11 |
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|
| 12 |
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| 13 |
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|
| 14 |
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],
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| 40 |
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| 41 |
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],
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| 44 |
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"TEMP": 310,
|
| 45 |
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"ENSEMBLE": "NPT",
|
| 46 |
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"FF": [
|
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"CHARMM36m"
|
| 48 |
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],
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| 49 |
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"WAT": "TIP3P",
|
| 50 |
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|
| 51 |
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},
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],
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"mdref": 0,
|
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| 96 |
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| 101 |
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| 110 |
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| 111 |
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| 113 |
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| 115 |
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| 117 |
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| 120 |
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| 123 |
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|
| 124 |
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"pocket_01.pdb",
|
| 125 |
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|
| 126 |
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|
| 127 |
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|
| 128 |
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"pocket_05.pdb",
|
| 129 |
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"pocket_06.pdb"
|
| 130 |
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],
|
| 131 |
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|
| 132 |
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|
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| 136 |
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| 137 |
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|
| 138 |
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|
| 139 |
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|
| 140 |
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| 141 |
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|
| 142 |
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|
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| 144 |
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],
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| 145 |
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"updateDate": "2025-07-23T12:43:43.107Z",
|
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"creationDate": "2025-07-22T15:37:14.000Z",
|
| 152 |
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"identifier": "A00G7"
|
| 153 |
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}
|
data/files/A00G7/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
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| 3 |
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data/files/A00G8/project.json
ADDED
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| 1 |
+
{
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| 2 |
+
"accession": "A00G8",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 7PS0",
|
| 6 |
+
"DESCRIPTION": "Antigen from Zhao test set, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"CONTACT": "[email protected]",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
+
"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
+
"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
+
"CITATION": "DynaRepo citation",
|
| 23 |
+
"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
+
"LINKS": null,
|
| 25 |
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"PDBIDS": [
|
| 26 |
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"7PS0"
|
| 27 |
+
],
|
| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P0DTC2"
|
| 31 |
+
],
|
| 32 |
+
"INPUT_LIGANDS": null,
|
| 33 |
+
"LIGANDS": [],
|
| 34 |
+
"LIGANDNAMES": null,
|
| 35 |
+
"PROTSEQ": [
|
| 36 |
+
"TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVKGFNCYFPLQSYGFQPTYGVGYQPYRVVVLSFELLHAPATVCGK"
|
| 37 |
+
],
|
| 38 |
+
"NUCLSEQ": [],
|
| 39 |
+
"DOMAINS": [
|
| 40 |
+
"Spike glycoprotein",
|
| 41 |
+
"Spike protein S1",
|
| 42 |
+
"BetaCoV S1-CTD",
|
| 43 |
+
"Disordered",
|
| 44 |
+
"Receptor-binding domain (RBD)",
|
| 45 |
+
"Integrin-binding motif;",
|
| 46 |
+
"Receptor-binding motif; binding to human ACE2",
|
| 47 |
+
"Immunodominant HLA epitope recognized by the CD8+; called NF9 peptide"
|
| 48 |
+
],
|
| 49 |
+
"FRAMESTEP": 0.1,
|
| 50 |
+
"TIMESTEP": 2,
|
| 51 |
+
"TEMP": 310,
|
| 52 |
+
"ENSEMBLE": "NPT",
|
| 53 |
+
"FF": [
|
| 54 |
+
"CHARMM36m"
|
| 55 |
+
],
|
| 56 |
+
"WAT": "TIP3P",
|
| 57 |
+
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|
| 58 |
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|
| 59 |
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|
| 60 |
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|
| 61 |
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"PROTRES": 195,
|
| 62 |
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"NUCLATS": 0,
|
| 63 |
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"NUCLRES": 0,
|
| 64 |
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"LIPIATS": 0,
|
| 65 |
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|
| 66 |
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|
| 67 |
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"CARBRES": 0,
|
| 68 |
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|
| 69 |
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|
| 70 |
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|
| 71 |
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|
| 72 |
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"COUNION": 0,
|
| 73 |
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"INTERACTIONS": [],
|
| 74 |
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"PBC_SELECTION": null,
|
| 75 |
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"CHAINNAMES": null,
|
| 76 |
+
"MEMBRANES": null,
|
| 77 |
+
"CUSTOMS": null,
|
| 78 |
+
"ORIENTATION": null,
|
| 79 |
+
"PTM": [],
|
| 80 |
+
"MULTIMERIC": null,
|
| 81 |
+
"COLLECTIONS": "dynarepo",
|
| 82 |
+
"WARNINGS": [],
|
| 83 |
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"BOXSIZEX": 9.12106,
|
| 84 |
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"BOXSIZEY": 9.12106,
|
| 85 |
+
"BOXSIZEZ": 6.44354,
|
| 86 |
+
"mdName": "replica 1",
|
| 87 |
+
"mdAtoms": 3021,
|
| 88 |
+
"mdFrames": 5001
|
| 89 |
+
},
|
| 90 |
+
"mds": [
|
| 91 |
+
"replica 1",
|
| 92 |
+
"replica 2",
|
| 93 |
+
"replica 3"
|
| 94 |
+
],
|
| 95 |
+
"mdref": 0,
|
| 96 |
+
"files": [
|
| 97 |
+
"topology.tpr",
|
| 98 |
+
"screenshot.jpg",
|
| 99 |
+
"trajectory.bin",
|
| 100 |
+
"pca_trajectory_01.bin",
|
| 101 |
+
"pca_trajectory_02.bin",
|
| 102 |
+
"pca_trajectory_03.bin",
|
| 103 |
+
"pca_trajectory_04.bin",
|
| 104 |
+
"pca_trajectory_05.bin",
|
| 105 |
+
"pca_trajectory_06.bin",
|
| 106 |
+
"pca_trajectory_07.bin",
|
| 107 |
+
"pca_trajectory_08.bin",
|
| 108 |
+
"pca_trajectory_09.bin",
|
| 109 |
+
"pca_trajectory_10.bin",
|
| 110 |
+
"pca_trajectory_11.bin",
|
| 111 |
+
"pca_trajectory_12.bin",
|
| 112 |
+
"pca_trajectory_13.bin",
|
| 113 |
+
"pca_trajectory_14.bin",
|
| 114 |
+
"pca_trajectory_15.bin",
|
| 115 |
+
"pca_trajectory_16.bin",
|
| 116 |
+
"structure.pdb",
|
| 117 |
+
"trajectory.xtc",
|
| 118 |
+
"clusters_00_screenshot_00.jpg",
|
| 119 |
+
"clusters_00_screenshot_01.jpg",
|
| 120 |
+
"clusters_00_screenshot_02.jpg",
|
| 121 |
+
"clusters_00_screenshot_03.jpg",
|
| 122 |
+
"clusters_00_screenshot_04.jpg",
|
| 123 |
+
"clusters_00_screenshot_05.jpg",
|
| 124 |
+
"clusters_00_screenshot_06.jpg",
|
| 125 |
+
"clusters_00_screenshot_07.jpg",
|
| 126 |
+
"clusters_00_screenshot_08.jpg",
|
| 127 |
+
"clusters_00_screenshot_09.jpg",
|
| 128 |
+
"clusters_00_screenshot_10.jpg",
|
| 129 |
+
"clusters_00_screenshot_11.jpg",
|
| 130 |
+
"clusters_00_screenshot_12.jpg",
|
| 131 |
+
"clusters_00_screenshot_13.jpg",
|
| 132 |
+
"clusters_00_screenshot_14.jpg",
|
| 133 |
+
"clusters_00_screenshot_15.jpg",
|
| 134 |
+
"clusters_00_screenshot_16.jpg",
|
| 135 |
+
"clusters_00_screenshot_17.jpg",
|
| 136 |
+
"clusters_00_screenshot_18.jpg",
|
| 137 |
+
"clusters_00_screenshot_19.jpg",
|
| 138 |
+
"pocket_01.pdb",
|
| 139 |
+
"pocket_02.pdb",
|
| 140 |
+
"pocket_03.pdb"
|
| 141 |
+
],
|
| 142 |
+
"analyses": [
|
| 143 |
+
"mem-map",
|
| 144 |
+
"clusters",
|
| 145 |
+
"clusters-00",
|
| 146 |
+
"fluctuation",
|
| 147 |
+
"pca",
|
| 148 |
+
"pockets",
|
| 149 |
+
"rgyr",
|
| 150 |
+
"rmsd-pairwise",
|
| 151 |
+
"rmsd-perres",
|
| 152 |
+
"rmsds",
|
| 153 |
+
"sasa",
|
| 154 |
+
"tmscores"
|
| 155 |
+
],
|
| 156 |
+
"updateDate": "2025-07-23T12:43:46.017Z",
|
| 157 |
+
"mdcount": 3,
|
| 158 |
+
"mdIndex": 0,
|
| 159 |
+
"mdNumber": 1,
|
| 160 |
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"refframe": 0,
|
| 161 |
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"internalId": "687fb193d8de476ba485d56c",
|
| 162 |
+
"creationDate": "2025-07-22T15:43:15.000Z",
|
| 163 |
+
"identifier": "A00G8"
|
| 164 |
+
}
|
data/files/A00G8/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A00G8", "accession": "A00G8", "published": true, "md_index": 0, "md_name": "replica 1", "analyses": ["mem-map", "clusters", "clusters-00", "fluctuation", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 7PS0", "DESCRIPTION": "Antigen from Zhao test set, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "[email protected]", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["7PS0"], "FORCED_REFERENCES": null, "REFERENCES": ["P0DTC2"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": 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data/files/A00G9/project.json
ADDED
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| 1 |
+
{
|
| 2 |
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"accession": "A00G9",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 7PS2",
|
| 6 |
+
"DESCRIPTION": "Antigen from Zhao test set, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
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"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
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],
|
| 12 |
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"GROUPS": [
|
| 13 |
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"Delta team, Inria center at the University of Lorraine"
|
| 14 |
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],
|
| 15 |
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"CONTACT": "[email protected]",
|
| 16 |
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"PROGRAM": "GROMACS",
|
| 17 |
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"VERSION": "2024.2",
|
| 18 |
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"TYPE": "trajectory",
|
| 19 |
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"METHOD": "Classical MD",
|
| 20 |
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"LICENSE": "Apache License 2.0",
|
| 21 |
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"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
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"CITATION": "DynaRepo citation",
|
| 23 |
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"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
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"LINKS": null,
|
| 25 |
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"PDBIDS": [
|
| 26 |
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"7PS2"
|
| 27 |
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],
|
| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
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"REFERENCES": [
|
| 30 |
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"P0DTC2"
|
| 31 |
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],
|
| 32 |
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"INPUT_LIGANDS": null,
|
| 33 |
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"LIGANDS": [],
|
| 34 |
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"LIGANDNAMES": null,
|
| 35 |
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"PROTSEQ": [
|
| 36 |
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"HHHHTNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVKGFNCYFPLQSYGFQPTYGVGYQPYRVVVLSFELLHAPATVC"
|
| 37 |
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],
|
| 38 |
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"NUCLSEQ": [],
|
| 39 |
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"DOMAINS": [
|
| 40 |
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"Spike glycoprotein",
|
| 41 |
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"Spike protein S1",
|
| 42 |
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"BetaCoV S1-CTD",
|
| 43 |
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"Disordered",
|
| 44 |
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"Receptor-binding domain (RBD)",
|
| 45 |
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"Integrin-binding motif;",
|
| 46 |
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"Receptor-binding motif; binding to human ACE2",
|
| 47 |
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"Immunodominant HLA epitope recognized by the CD8+; called NF9 peptide"
|
| 48 |
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],
|
| 49 |
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"FRAMESTEP": 0.1,
|
| 50 |
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"TIMESTEP": 2,
|
| 51 |
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"TEMP": 310,
|
| 52 |
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"ENSEMBLE": "NPT",
|
| 53 |
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"FF": [
|
| 54 |
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"CHARMM36m"
|
| 55 |
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],
|
| 56 |
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"WAT": "TIP3P",
|
| 57 |
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"BOXTYPE": "Dodecahedron",
|
| 58 |
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"SYSTATS": 3060,
|
| 59 |
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"SYSTRES": 197,
|
| 60 |
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"PROTATS": 3060,
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| 61 |
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"PROTRES": 197,
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| 62 |
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"NUCLATS": 0,
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| 63 |
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| 64 |
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| 65 |
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| 66 |
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| 69 |
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| 70 |
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"COUNCAT": 0,
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| 71 |
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"COUNANI": 0,
|
| 72 |
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"COUNION": 0,
|
| 73 |
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"INTERACTIONS": [],
|
| 74 |
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"PBC_SELECTION": null,
|
| 75 |
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"CHAINNAMES": null,
|
| 76 |
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"MEMBRANES": null,
|
| 77 |
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"CUSTOMS": null,
|
| 78 |
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"ORIENTATION": null,
|
| 79 |
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"PTM": [],
|
| 80 |
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"MULTIMERIC": null,
|
| 81 |
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"COLLECTIONS": "dynarepo",
|
| 82 |
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"WARNINGS": [],
|
| 83 |
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"BOXSIZEX": 9.09121,
|
| 84 |
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"BOXSIZEY": 9.09121,
|
| 85 |
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"BOXSIZEZ": 6.43977,
|
| 86 |
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"mdName": "replica 1",
|
| 87 |
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"mdAtoms": 3060,
|
| 88 |
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"mdFrames": 5001
|
| 89 |
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},
|
| 90 |
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"mds": [
|
| 91 |
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"replica 1",
|
| 92 |
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"replica 2",
|
| 93 |
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"replica 3"
|
| 94 |
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],
|
| 95 |
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"mdref": 0,
|
| 96 |
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"files": [
|
| 97 |
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|
| 98 |
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|
| 99 |
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| 100 |
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| 101 |
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| 102 |
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| 103 |
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| 104 |
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| 105 |
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| 106 |
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| 107 |
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| 109 |
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| 110 |
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| 111 |
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| 112 |
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| 113 |
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|
| 114 |
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"structure.pdb",
|
| 115 |
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|
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|
| 128 |
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| 129 |
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|
| 130 |
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|
| 131 |
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|
| 132 |
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|
| 133 |
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| 134 |
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|
| 135 |
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|
| 136 |
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"clusters_00_screenshot_20.jpg",
|
| 137 |
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"pocket_01.pdb",
|
| 138 |
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"pocket_02.pdb",
|
| 139 |
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"pocket_03.pdb",
|
| 140 |
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"pocket_04.pdb"
|
| 141 |
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],
|
| 142 |
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"analyses": [
|
| 143 |
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"mem-map",
|
| 144 |
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|
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|
| 146 |
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| 147 |
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|
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|
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|
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|
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|
| 152 |
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| 153 |
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|
| 154 |
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"tmscores"
|
| 155 |
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],
|
| 156 |
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"updateDate": "2025-07-23T12:43:48.792Z",
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"internalId": "687fb20cd7a98bc321bcd667",
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"identifier": "A00G9"
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}
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| 3 |
+
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| 1 |
+
{
|
| 2 |
+
"accession": "A00GA",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 7PS4",
|
| 6 |
+
"DESCRIPTION": "Antigen from Zhao test set, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"CONTACT": "[email protected]",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
+
"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
+
"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
+
"CITATION": "DynaRepo citation",
|
| 23 |
+
"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
+
"LINKS": null,
|
| 25 |
+
"PDBIDS": [
|
| 26 |
+
"7PS4"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P0DTC2"
|
| 31 |
+
],
|
| 32 |
+
"INPUT_LIGANDS": null,
|
| 33 |
+
"LIGANDS": [],
|
| 34 |
+
"LIGANDNAMES": null,
|
| 35 |
+
"PROTSEQ": [
|
| 36 |
+
"TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVKGFNCYFPLQSYGFQPTYGVGYQPYRVVVLSFELLHAPATVCGK"
|
| 37 |
+
],
|
| 38 |
+
"NUCLSEQ": [],
|
| 39 |
+
"DOMAINS": [
|
| 40 |
+
"Spike glycoprotein",
|
| 41 |
+
"Spike protein S1",
|
| 42 |
+
"BetaCoV S1-CTD",
|
| 43 |
+
"Disordered",
|
| 44 |
+
"Receptor-binding domain (RBD)",
|
| 45 |
+
"Integrin-binding motif;",
|
| 46 |
+
"Receptor-binding motif; binding to human ACE2",
|
| 47 |
+
"Immunodominant HLA epitope recognized by the CD8+; called NF9 peptide"
|
| 48 |
+
],
|
| 49 |
+
"FRAMESTEP": 0.1,
|
| 50 |
+
"TIMESTEP": 2,
|
| 51 |
+
"TEMP": 310,
|
| 52 |
+
"ENSEMBLE": "NPT",
|
| 53 |
+
"FF": [
|
| 54 |
+
"CHARMM36m"
|
| 55 |
+
],
|
| 56 |
+
"WAT": "TIP3P",
|
| 57 |
+
"BOXTYPE": "Dodecahedron",
|
| 58 |
+
"SYSTATS": 3021,
|
| 59 |
+
"SYSTRES": 195,
|
| 60 |
+
"PROTATS": 3021,
|
| 61 |
+
"PROTRES": 195,
|
| 62 |
+
"NUCLATS": 0,
|
| 63 |
+
"NUCLRES": 0,
|
| 64 |
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"LIPIATS": 0,
|
| 65 |
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"LIPIRES": 0,
|
| 66 |
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"CARBATS": 0,
|
| 67 |
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"CARBRES": 0,
|
| 68 |
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"SOLVATS": 0,
|
| 69 |
+
"SOLVRES": 0,
|
| 70 |
+
"COUNCAT": 0,
|
| 71 |
+
"COUNANI": 0,
|
| 72 |
+
"COUNION": 0,
|
| 73 |
+
"INTERACTIONS": [],
|
| 74 |
+
"PBC_SELECTION": null,
|
| 75 |
+
"CHAINNAMES": null,
|
| 76 |
+
"MEMBRANES": null,
|
| 77 |
+
"CUSTOMS": null,
|
| 78 |
+
"ORIENTATION": null,
|
| 79 |
+
"PTM": [],
|
| 80 |
+
"MULTIMERIC": null,
|
| 81 |
+
"COLLECTIONS": "dynarepo",
|
| 82 |
+
"WARNINGS": [],
|
| 83 |
+
"BOXSIZEX": 9.02359,
|
| 84 |
+
"BOXSIZEY": 9.02359,
|
| 85 |
+
"BOXSIZEZ": 6.3773,
|
| 86 |
+
"mdName": "replica 1",
|
| 87 |
+
"mdAtoms": 3021,
|
| 88 |
+
"mdFrames": 5001
|
| 89 |
+
},
|
| 90 |
+
"mds": [
|
| 91 |
+
"replica 1",
|
| 92 |
+
"replica 2",
|
| 93 |
+
"replica 3"
|
| 94 |
+
],
|
| 95 |
+
"mdref": 0,
|
| 96 |
+
"files": [
|
| 97 |
+
"topology.tpr",
|
| 98 |
+
"screenshot.jpg",
|
| 99 |
+
"trajectory.bin",
|
| 100 |
+
"pca_trajectory_01.bin",
|
| 101 |
+
"pca_trajectory_02.bin",
|
| 102 |
+
"pca_trajectory_03.bin",
|
| 103 |
+
"pca_trajectory_04.bin",
|
| 104 |
+
"pca_trajectory_05.bin",
|
| 105 |
+
"pca_trajectory_06.bin",
|
| 106 |
+
"pca_trajectory_07.bin",
|
| 107 |
+
"pca_trajectory_08.bin",
|
| 108 |
+
"pca_trajectory_09.bin",
|
| 109 |
+
"pca_trajectory_10.bin",
|
| 110 |
+
"pca_trajectory_11.bin",
|
| 111 |
+
"pca_trajectory_12.bin",
|
| 112 |
+
"pca_trajectory_13.bin",
|
| 113 |
+
"pca_trajectory_14.bin",
|
| 114 |
+
"structure.pdb",
|
| 115 |
+
"trajectory.xtc",
|
| 116 |
+
"clusters_00_screenshot_00.jpg",
|
| 117 |
+
"clusters_00_screenshot_01.jpg",
|
| 118 |
+
"clusters_00_screenshot_02.jpg",
|
| 119 |
+
"clusters_00_screenshot_03.jpg",
|
| 120 |
+
"clusters_00_screenshot_04.jpg",
|
| 121 |
+
"clusters_00_screenshot_05.jpg",
|
| 122 |
+
"clusters_00_screenshot_06.jpg",
|
| 123 |
+
"clusters_00_screenshot_07.jpg",
|
| 124 |
+
"clusters_00_screenshot_08.jpg",
|
| 125 |
+
"clusters_00_screenshot_09.jpg",
|
| 126 |
+
"clusters_00_screenshot_10.jpg",
|
| 127 |
+
"clusters_00_screenshot_11.jpg",
|
| 128 |
+
"clusters_00_screenshot_12.jpg",
|
| 129 |
+
"clusters_00_screenshot_13.jpg",
|
| 130 |
+
"clusters_00_screenshot_14.jpg",
|
| 131 |
+
"clusters_00_screenshot_15.jpg",
|
| 132 |
+
"clusters_00_screenshot_16.jpg",
|
| 133 |
+
"clusters_00_screenshot_17.jpg",
|
| 134 |
+
"clusters_00_screenshot_18.jpg",
|
| 135 |
+
"clusters_00_screenshot_19.jpg",
|
| 136 |
+
"pocket_01.pdb",
|
| 137 |
+
"pocket_02.pdb",
|
| 138 |
+
"pocket_03.pdb"
|
| 139 |
+
],
|
| 140 |
+
"analyses": [
|
| 141 |
+
"mem-map",
|
| 142 |
+
"clusters",
|
| 143 |
+
"clusters-00",
|
| 144 |
+
"fluctuation",
|
| 145 |
+
"pca",
|
| 146 |
+
"pockets",
|
| 147 |
+
"rgyr",
|
| 148 |
+
"rmsd-pairwise",
|
| 149 |
+
"rmsd-perres",
|
| 150 |
+
"rmsds",
|
| 151 |
+
"sasa",
|
| 152 |
+
"tmscores"
|
| 153 |
+
],
|
| 154 |
+
"updateDate": "2025-07-23T12:45:33.707Z",
|
| 155 |
+
"mdcount": 3,
|
| 156 |
+
"mdIndex": 0,
|
| 157 |
+
"mdNumber": 1,
|
| 158 |
+
"refframe": 0,
|
| 159 |
+
"internalId": "687fb2878d233c57a8da93dc",
|
| 160 |
+
"creationDate": "2025-07-22T15:47:19.000Z",
|
| 161 |
+
"identifier": "A00GA"
|
| 162 |
+
}
|
data/files/A00GA/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A00GA", "accession": "A00GA", "published": true, "md_index": 0, "md_name": "replica 1", "analyses": ["mem-map", "clusters", "clusters-00", "fluctuation", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 7PS4", "DESCRIPTION": "Antigen from Zhao test set, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "[email protected]", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["7PS4"], "FORCED_REFERENCES": null, "REFERENCES": ["P0DTC2"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": 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| 3 |
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data/files/A00GB/project.json
ADDED
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| 1 |
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{
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| 2 |
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"accession": "A00GB",
|
| 3 |
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"published": true,
|
| 4 |
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"metadata": {
|
| 5 |
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"NAME": "Dynarepo 7PS6",
|
| 6 |
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"DESCRIPTION": "Antigen from Zhao test set, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
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"AUTHORS": [
|
| 8 |
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"Omid Mokhtari",
|
| 9 |
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"Hamed Khakzad",
|
| 10 |
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"Yasaman Karami"
|
| 11 |
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],
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| 12 |
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|
| 13 |
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|
| 14 |
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],
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| 15 |
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"CONTACT": "[email protected]",
|
| 16 |
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|
| 17 |
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"VERSION": "2024.2",
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| 18 |
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"TYPE": "trajectory",
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| 19 |
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"METHOD": "Classical MD",
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| 20 |
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"LICENSE": "Apache License 2.0",
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| 21 |
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"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
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| 22 |
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"CITATION": "DynaRepo citation",
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| 23 |
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"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
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"LINKS": null,
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| 25 |
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"PDBIDS": [
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| 26 |
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"7PS6"
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| 27 |
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],
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| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
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"REFERENCES": [
|
| 30 |
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"P0DTC2"
|
| 31 |
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],
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| 32 |
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"INPUT_LIGANDS": null,
|
| 33 |
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"LIGANDS": [],
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| 34 |
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"LIGANDNAMES": null,
|
| 35 |
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"PROTSEQ": [
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| 36 |
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"NLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVKGFNCYFPLQSYGFQPTYGVGYQPYRVVVLSF"
|
| 37 |
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],
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| 38 |
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"NUCLSEQ": [],
|
| 39 |
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"DOMAINS": [
|
| 40 |
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"Spike glycoprotein",
|
| 41 |
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"Spike protein S1",
|
| 42 |
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"BetaCoV S1-CTD",
|
| 43 |
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"Disordered",
|
| 44 |
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"Receptor-binding domain (RBD)",
|
| 45 |
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"Integrin-binding motif;",
|
| 46 |
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"Receptor-binding motif; binding to human ACE2",
|
| 47 |
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"Immunodominant HLA epitope recognized by the CD8+; called NF9 peptide"
|
| 48 |
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],
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| 49 |
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|
| 50 |
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| 51 |
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"TEMP": 310,
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| 52 |
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"ENSEMBLE": "NPT",
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| 53 |
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"FF": [
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| 54 |
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"CHARMM36m"
|
| 55 |
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],
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| 56 |
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"WAT": "TIP3P",
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| 57 |
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| 58 |
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| 59 |
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| 60 |
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| 72 |
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"COLLECTIONS": "dynarepo",
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| 82 |
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| 83 |
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| 87 |
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| 89 |
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},
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| 90 |
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"mds": [
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| 91 |
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"replica 1",
|
| 92 |
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"replica 2",
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|
| 94 |
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],
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| 135 |
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| 136 |
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| 137 |
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],
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"analyses": [
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| 150 |
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"tmscores"
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],
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+
"updateDate": "2025-07-23T12:45:38.045Z",
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| 153 |
+
"mdcount": 3,
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| 154 |
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"mdIndex": 0,
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+
"mdNumber": 1,
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"refframe": 0,
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+
"internalId": "687fb303a3557ef02dc46dc9",
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| 158 |
+
"creationDate": "2025-07-22T15:49:23.000Z",
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+
"identifier": "A00GB"
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+
}
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data/files/A00GB/records.jsonl
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| 3 |
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|
data/files/A00GC/project.json
ADDED
|
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| 1 |
+
{
|
| 2 |
+
"accession": "A00GC",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 7Q0G",
|
| 6 |
+
"DESCRIPTION": "Antigen from Zhao test set, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
+
"GROUPS": [
|
| 13 |
+
"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
+
"CONTACT": "[email protected]",
|
| 16 |
+
"PROGRAM": "GROMACS",
|
| 17 |
+
"VERSION": "2024.2",
|
| 18 |
+
"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
+
"LICENSE": "Apache License 2.0",
|
| 21 |
+
"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
+
"CITATION": "DynaRepo citation",
|
| 23 |
+
"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
+
"LINKS": null,
|
| 25 |
+
"PDBIDS": [
|
| 26 |
+
"7Q0G"
|
| 27 |
+
],
|
| 28 |
+
"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P0DTC2"
|
| 31 |
+
],
|
| 32 |
+
"INPUT_LIGANDS": null,
|
| 33 |
+
"LIGANDS": [],
|
| 34 |
+
"LIGANDNAMES": null,
|
| 35 |
+
"PROTSEQ": [
|
| 36 |
+
"TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVKGFNCYFPLQSYGFQPTYGVGYQPYRVVVLSFELLHAPATVCGKK"
|
| 37 |
+
],
|
| 38 |
+
"NUCLSEQ": [],
|
| 39 |
+
"DOMAINS": [
|
| 40 |
+
"Spike glycoprotein",
|
| 41 |
+
"Spike protein S1",
|
| 42 |
+
"BetaCoV S1-CTD",
|
| 43 |
+
"Disordered",
|
| 44 |
+
"Receptor-binding domain (RBD)",
|
| 45 |
+
"Integrin-binding motif;",
|
| 46 |
+
"Receptor-binding motif; binding to human ACE2",
|
| 47 |
+
"Immunodominant HLA epitope recognized by the CD8+; called NF9 peptide"
|
| 48 |
+
],
|
| 49 |
+
"FRAMESTEP": 0.1,
|
| 50 |
+
"TIMESTEP": 2,
|
| 51 |
+
"TEMP": 310,
|
| 52 |
+
"ENSEMBLE": "NPT",
|
| 53 |
+
"FF": [
|
| 54 |
+
"CHARMM36m"
|
| 55 |
+
],
|
| 56 |
+
"WAT": "TIP3P",
|
| 57 |
+
"BOXTYPE": "Dodecahedron",
|
| 58 |
+
"SYSTATS": 3043,
|
| 59 |
+
"SYSTRES": 196,
|
| 60 |
+
"PROTATS": 3043,
|
| 61 |
+
"PROTRES": 196,
|
| 62 |
+
"NUCLATS": 0,
|
| 63 |
+
"NUCLRES": 0,
|
| 64 |
+
"LIPIATS": 0,
|
| 65 |
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"LIPIRES": 0,
|
| 66 |
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|
| 67 |
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|
| 68 |
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|
| 69 |
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|
| 70 |
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"COUNCAT": 0,
|
| 71 |
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"COUNANI": 0,
|
| 72 |
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|
| 73 |
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|
| 74 |
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|
| 75 |
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"CHAINNAMES": null,
|
| 76 |
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"MEMBRANES": null,
|
| 77 |
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"CUSTOMS": null,
|
| 78 |
+
"ORIENTATION": null,
|
| 79 |
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"PTM": [],
|
| 80 |
+
"MULTIMERIC": null,
|
| 81 |
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"COLLECTIONS": "dynarepo",
|
| 82 |
+
"WARNINGS": [],
|
| 83 |
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"BOXSIZEX": 9.24104,
|
| 84 |
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"BOXSIZEY": 9.24104,
|
| 85 |
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"BOXSIZEZ": 6.56126,
|
| 86 |
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"mdName": "replica 1",
|
| 87 |
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"mdAtoms": 3043,
|
| 88 |
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"mdFrames": 5001
|
| 89 |
+
},
|
| 90 |
+
"mds": [
|
| 91 |
+
"replica 1",
|
| 92 |
+
"replica 2",
|
| 93 |
+
"replica 3"
|
| 94 |
+
],
|
| 95 |
+
"mdref": 0,
|
| 96 |
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"files": [
|
| 97 |
+
"topology.tpr",
|
| 98 |
+
"screenshot.jpg",
|
| 99 |
+
"trajectory.bin",
|
| 100 |
+
"pca_trajectory_01.bin",
|
| 101 |
+
"pca_trajectory_02.bin",
|
| 102 |
+
"pca_trajectory_03.bin",
|
| 103 |
+
"pca_trajectory_04.bin",
|
| 104 |
+
"pca_trajectory_05.bin",
|
| 105 |
+
"pca_trajectory_06.bin",
|
| 106 |
+
"pca_trajectory_07.bin",
|
| 107 |
+
"pca_trajectory_08.bin",
|
| 108 |
+
"pca_trajectory_09.bin",
|
| 109 |
+
"pca_trajectory_10.bin",
|
| 110 |
+
"pca_trajectory_11.bin",
|
| 111 |
+
"pca_trajectory_12.bin",
|
| 112 |
+
"pca_trajectory_13.bin",
|
| 113 |
+
"pca_trajectory_14.bin",
|
| 114 |
+
"pca_trajectory_15.bin",
|
| 115 |
+
"pca_trajectory_16.bin",
|
| 116 |
+
"pca_trajectory_17.bin",
|
| 117 |
+
"structure.pdb",
|
| 118 |
+
"trajectory.xtc",
|
| 119 |
+
"clusters_00_screenshot_00.jpg",
|
| 120 |
+
"clusters_00_screenshot_01.jpg",
|
| 121 |
+
"clusters_00_screenshot_02.jpg",
|
| 122 |
+
"clusters_00_screenshot_03.jpg",
|
| 123 |
+
"clusters_00_screenshot_04.jpg",
|
| 124 |
+
"clusters_00_screenshot_05.jpg",
|
| 125 |
+
"clusters_00_screenshot_06.jpg",
|
| 126 |
+
"clusters_00_screenshot_07.jpg",
|
| 127 |
+
"clusters_00_screenshot_08.jpg",
|
| 128 |
+
"clusters_00_screenshot_09.jpg",
|
| 129 |
+
"clusters_00_screenshot_10.jpg",
|
| 130 |
+
"clusters_00_screenshot_11.jpg",
|
| 131 |
+
"clusters_00_screenshot_12.jpg",
|
| 132 |
+
"clusters_00_screenshot_13.jpg",
|
| 133 |
+
"clusters_00_screenshot_14.jpg",
|
| 134 |
+
"clusters_00_screenshot_15.jpg",
|
| 135 |
+
"clusters_00_screenshot_16.jpg",
|
| 136 |
+
"clusters_00_screenshot_17.jpg",
|
| 137 |
+
"clusters_00_screenshot_18.jpg",
|
| 138 |
+
"clusters_00_screenshot_19.jpg",
|
| 139 |
+
"clusters_00_screenshot_20.jpg",
|
| 140 |
+
"clusters_00_screenshot_21.jpg",
|
| 141 |
+
"clusters_00_screenshot_22.jpg",
|
| 142 |
+
"pocket_01.pdb",
|
| 143 |
+
"pocket_02.pdb",
|
| 144 |
+
"pocket_03.pdb"
|
| 145 |
+
],
|
| 146 |
+
"analyses": [
|
| 147 |
+
"mem-map",
|
| 148 |
+
"clusters",
|
| 149 |
+
"clusters-00",
|
| 150 |
+
"fluctuation",
|
| 151 |
+
"pca",
|
| 152 |
+
"pockets",
|
| 153 |
+
"rgyr",
|
| 154 |
+
"rmsd-pairwise",
|
| 155 |
+
"rmsd-perres",
|
| 156 |
+
"rmsds",
|
| 157 |
+
"sasa",
|
| 158 |
+
"tmscores"
|
| 159 |
+
],
|
| 160 |
+
"updateDate": "2025-07-23T12:45:41.286Z",
|
| 161 |
+
"mdcount": 3,
|
| 162 |
+
"mdIndex": 0,
|
| 163 |
+
"mdNumber": 1,
|
| 164 |
+
"refframe": 0,
|
| 165 |
+
"internalId": "687fb382e7c30ad66adfda28",
|
| 166 |
+
"creationDate": "2025-07-22T15:51:30.000Z",
|
| 167 |
+
"identifier": "A00GC"
|
| 168 |
+
}
|
data/files/A00GC/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{"project_identifier": "A00GC", "accession": "A00GC", "published": true, "md_index": 0, "md_name": "replica 1", "analyses": ["mem-map", "clusters", "clusters-00", "fluctuation", "pca", "pockets", "rgyr", "rmsd-pairwise", "rmsd-perres", "rmsds", "sasa", "tmscores"], "chains": [], "metadata": {"NAME": "Dynarepo 7Q0G", "DESCRIPTION": "Antigen from Zhao test set, Classical MD simulations, 3 replicates of 500 ns", "AUTHORS": ["Omid Mokhtari", "Hamed Khakzad", "Yasaman Karami"], "GROUPS": ["Delta team, Inria center at the University of Lorraine"], "CONTACT": "[email protected]", "PROGRAM": "GROMACS", "VERSION": "2024.2", "TYPE": "trajectory", "METHOD": "Classical MD", "LICENSE": "Apache License 2.0", "LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0", "CITATION": "DynaRepo citation", "THANKS": "DynaRepo Acknowledgements", "LINKS": null, "PDBIDS": ["7Q0G"], "FORCED_REFERENCES": null, "REFERENCES": ["P0DTC2"], "INPUT_LIGANDS": null, "LIGANDS": [], "LIGANDNAMES": null, "PROTSEQ": 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data/files/A00GD/project.json
ADDED
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@@ -0,0 +1,164 @@
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|
| 1 |
+
{
|
| 2 |
+
"accession": "A00GD",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 7Q0I",
|
| 6 |
+
"DESCRIPTION": "Antigen from Zhao test set, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
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"GROUPS": [
|
| 13 |
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|
| 14 |
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|
| 15 |
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|
| 16 |
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|
| 17 |
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|
| 18 |
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|
| 19 |
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|
| 20 |
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"LICENSE": "Apache License 2.0",
|
| 21 |
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|
| 22 |
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|
| 23 |
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"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
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|
| 25 |
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|
| 26 |
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"7Q0I"
|
| 27 |
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],
|
| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
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"REFERENCES": [
|
| 30 |
+
"P0DTC2"
|
| 31 |
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],
|
| 32 |
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"INPUT_LIGANDS": null,
|
| 33 |
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|
| 34 |
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|
| 35 |
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|
| 36 |
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|
| 37 |
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],
|
| 38 |
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"NUCLSEQ": [],
|
| 39 |
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"DOMAINS": [
|
| 40 |
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"Spike glycoprotein",
|
| 41 |
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"Spike protein S1",
|
| 42 |
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"BetaCoV S1-NTD",
|
| 43 |
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"Disordered",
|
| 44 |
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"Putative superantigen; may bind T-cell receptor alpha/TRAC"
|
| 45 |
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],
|
| 46 |
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|
| 47 |
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|
| 48 |
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|
| 49 |
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|
| 50 |
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"FF": [
|
| 51 |
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"CHARMM36m"
|
| 52 |
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],
|
| 53 |
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|
| 54 |
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|
| 55 |
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|
| 56 |
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|
| 57 |
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| 58 |
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| 59 |
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| 64 |
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| 65 |
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| 67 |
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| 68 |
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| 69 |
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|
| 70 |
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| 71 |
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| 72 |
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| 73 |
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|
| 74 |
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| 75 |
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| 76 |
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| 77 |
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| 78 |
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"COLLECTIONS": "dynarepo",
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| 79 |
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|
| 80 |
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"BOXSIZEX": 9.70598,
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| 81 |
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"BOXSIZEY": 9.70598,
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| 82 |
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| 83 |
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"mdName": "replica 1",
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| 84 |
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| 85 |
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| 86 |
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},
|
| 87 |
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"mds": [
|
| 88 |
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"replica 1",
|
| 89 |
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"replica 2",
|
| 90 |
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"replica 3"
|
| 91 |
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],
|
| 92 |
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"mdref": 0,
|
| 93 |
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"files": [
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| 94 |
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| 97 |
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| 99 |
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| 100 |
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| 101 |
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| 106 |
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"pca_trajectory_10.bin",
|
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+
"pca_trajectory_11.bin",
|
| 108 |
+
"pca_trajectory_12.bin",
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| 109 |
+
"pca_trajectory_13.bin",
|
| 110 |
+
"pca_trajectory_14.bin",
|
| 111 |
+
"structure.pdb",
|
| 112 |
+
"trajectory.xtc",
|
| 113 |
+
"clusters_00_screenshot_00.jpg",
|
| 114 |
+
"clusters_00_screenshot_01.jpg",
|
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+
"clusters_00_screenshot_02.jpg",
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| 116 |
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"clusters_00_screenshot_03.jpg",
|
| 117 |
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"clusters_00_screenshot_04.jpg",
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"clusters_00_screenshot_05.jpg",
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"clusters_00_screenshot_06.jpg",
|
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"clusters_00_screenshot_07.jpg",
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"clusters_00_screenshot_08.jpg",
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"clusters_00_screenshot_09.jpg",
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"clusters_00_screenshot_10.jpg",
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"clusters_00_screenshot_11.jpg",
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"clusters_00_screenshot_12.jpg",
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"clusters_00_screenshot_13.jpg",
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"clusters_00_screenshot_14.jpg",
|
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"clusters_00_screenshot_15.jpg",
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"clusters_00_screenshot_16.jpg",
|
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"clusters_00_screenshot_17.jpg",
|
| 131 |
+
"clusters_00_screenshot_18.jpg",
|
| 132 |
+
"clusters_00_screenshot_19.jpg",
|
| 133 |
+
"pocket_01.pdb",
|
| 134 |
+
"pocket_02.pdb",
|
| 135 |
+
"pocket_03.pdb",
|
| 136 |
+
"pocket_04.pdb",
|
| 137 |
+
"pocket_05.pdb",
|
| 138 |
+
"pocket_06.pdb",
|
| 139 |
+
"pocket_07.pdb",
|
| 140 |
+
"pocket_08.pdb"
|
| 141 |
+
],
|
| 142 |
+
"analyses": [
|
| 143 |
+
"mem-map",
|
| 144 |
+
"clusters",
|
| 145 |
+
"clusters-00",
|
| 146 |
+
"fluctuation",
|
| 147 |
+
"pca",
|
| 148 |
+
"pockets",
|
| 149 |
+
"rgyr",
|
| 150 |
+
"rmsd-pairwise",
|
| 151 |
+
"rmsd-perres",
|
| 152 |
+
"rmsds",
|
| 153 |
+
"sasa",
|
| 154 |
+
"tmscores"
|
| 155 |
+
],
|
| 156 |
+
"updateDate": "2025-07-23T12:45:44.791Z",
|
| 157 |
+
"mdcount": 3,
|
| 158 |
+
"mdIndex": 0,
|
| 159 |
+
"mdNumber": 1,
|
| 160 |
+
"refframe": 0,
|
| 161 |
+
"internalId": "687fb407bd5533d37c3b5e4d",
|
| 162 |
+
"creationDate": "2025-07-22T15:53:43.000Z",
|
| 163 |
+
"identifier": "A00GD"
|
| 164 |
+
}
|
data/files/A00GD/records.jsonl
ADDED
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data/files/A00GE/project.json
ADDED
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@@ -0,0 +1,155 @@
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| 1 |
+
{
|
| 2 |
+
"accession": "A00GE",
|
| 3 |
+
"published": true,
|
| 4 |
+
"metadata": {
|
| 5 |
+
"NAME": "Dynarepo 7S0E",
|
| 6 |
+
"DESCRIPTION": "Antigen from Zhao test set, Classical MD simulations, 3 replicates of 500 ns",
|
| 7 |
+
"AUTHORS": [
|
| 8 |
+
"Omid Mokhtari",
|
| 9 |
+
"Hamed Khakzad",
|
| 10 |
+
"Yasaman Karami"
|
| 11 |
+
],
|
| 12 |
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"GROUPS": [
|
| 13 |
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"Delta team, Inria center at the University of Lorraine"
|
| 14 |
+
],
|
| 15 |
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"CONTACT": "[email protected]",
|
| 16 |
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"PROGRAM": "GROMACS",
|
| 17 |
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"VERSION": "2024.2",
|
| 18 |
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"TYPE": "trajectory",
|
| 19 |
+
"METHOD": "Classical MD",
|
| 20 |
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"LICENSE": "Apache License 2.0",
|
| 21 |
+
"LINKCENSE": "https://www.apache.org/licenses/LICENSE-2.0",
|
| 22 |
+
"CITATION": "DynaRepo citation",
|
| 23 |
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"THANKS": "DynaRepo Acknowledgements",
|
| 24 |
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"LINKS": null,
|
| 25 |
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"PDBIDS": [
|
| 26 |
+
"7S0E"
|
| 27 |
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],
|
| 28 |
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"FORCED_REFERENCES": null,
|
| 29 |
+
"REFERENCES": [
|
| 30 |
+
"P0DTC2"
|
| 31 |
+
],
|
| 32 |
+
"INPUT_LIGANDS": null,
|
| 33 |
+
"LIGANDS": [],
|
| 34 |
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"LIGANDNAMES": null,
|
| 35 |
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"PROTSEQ": [
|
| 36 |
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"SSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPASVASQSIIAYTMSLG"
|
| 37 |
+
],
|
| 38 |
+
"NUCLSEQ": [],
|
| 39 |
+
"DOMAINS": [
|
| 40 |
+
"Spike glycoprotein",
|
| 41 |
+
"Spike protein S1",
|
| 42 |
+
"Spike protein S2",
|
| 43 |
+
"BetaCoV S1-NTD",
|
| 44 |
+
"BetaCoV S1-CTD",
|
| 45 |
+
"Disordered",
|
| 46 |
+
"Putative superantigen; may bind T-cell receptor alpha/TRAC",
|
| 47 |
+
"Receptor-binding domain (RBD)",
|
| 48 |
+
"Integrin-binding motif;",
|
| 49 |
+
"Receptor-binding motif; binding to human ACE2",
|
| 50 |
+
"Immunodominant HLA epitope recognized by the CD8+; called NF9 peptide",
|
| 51 |
+
"Putative superantigen; may bind T-cell receptor beta/TRBC1",
|
| 52 |
+
"Cleavage; by host furin"
|
| 53 |
+
],
|
| 54 |
+
"FRAMESTEP": 0.1,
|
| 55 |
+
"TIMESTEP": 2,
|
| 56 |
+
"TEMP": 310,
|
| 57 |
+
"ENSEMBLE": "NPT",
|
| 58 |
+
"FF": [
|
| 59 |
+
"CHARMM36m"
|
| 60 |
+
],
|
| 61 |
+
"WAT": "TIP3P",
|
| 62 |
+
"BOXTYPE": "Dodecahedron",
|
| 63 |
+
"SYSTATS": 10607,
|
| 64 |
+
"SYSTRES": 686,
|
| 65 |
+
"PROTATS": 10607,
|
| 66 |
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"PROTRES": 686,
|
| 67 |
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"NUCLATS": 0,
|
| 68 |
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"NUCLRES": 0,
|
| 69 |
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"LIPIATS": 0,
|
| 70 |
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"LIPIRES": 0,
|
| 71 |
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"CARBATS": 0,
|
| 72 |
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"CARBRES": 0,
|
| 73 |
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"SOLVATS": 0,
|
| 74 |
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"SOLVRES": 0,
|
| 75 |
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"COUNCAT": 0,
|
| 76 |
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"COUNANI": 0,
|
| 77 |
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"COUNION": 0,
|
| 78 |
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"INTERACTIONS": [],
|
| 79 |
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"PBC_SELECTION": null,
|
| 80 |
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"CHAINNAMES": null,
|
| 81 |
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"MEMBRANES": null,
|
| 82 |
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"CUSTOMS": null,
|
| 83 |
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"ORIENTATION": null,
|
| 84 |
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"PTM": [],
|
| 85 |
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"MULTIMERIC": null,
|
| 86 |
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"COLLECTIONS": "dynarepo",
|
| 87 |
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"WARNINGS": [],
|
| 88 |
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"BOXSIZEX": 15.2104,
|
| 89 |
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"BOXSIZEY": 15.2104,
|
| 90 |
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"BOXSIZEZ": 10.7817,
|
| 91 |
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"mdName": "replica 1",
|
| 92 |
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"mdAtoms": 10607,
|
| 93 |
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"mdFrames": 5001
|
| 94 |
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},
|
| 95 |
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"mds": [
|
| 96 |
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"replica 1",
|
| 97 |
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"replica 2",
|
| 98 |
+
"replica 3"
|
| 99 |
+
],
|
| 100 |
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"mdref": 0,
|
| 101 |
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"files": [
|
| 102 |
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"topology.tpr",
|
| 103 |
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"screenshot.jpg",
|
| 104 |
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"trajectory.bin",
|
| 105 |
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"pca_trajectory_01.bin",
|
| 106 |
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"pca_trajectory_02.bin",
|
| 107 |
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"pca_trajectory_03.bin",
|
| 108 |
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"pca_trajectory_04.bin",
|
| 109 |
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"pca_trajectory_05.bin",
|
| 110 |
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"structure.pdb",
|
| 111 |
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"trajectory.xtc",
|
| 112 |
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"clusters_00_screenshot_00.jpg",
|
| 113 |
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"clusters_00_screenshot_01.jpg",
|
| 114 |
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"clusters_00_screenshot_02.jpg",
|
| 115 |
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"clusters_00_screenshot_03.jpg",
|
| 116 |
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"clusters_00_screenshot_04.jpg",
|
| 117 |
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"clusters_00_screenshot_05.jpg",
|
| 118 |
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"clusters_00_screenshot_06.jpg",
|
| 119 |
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|
| 120 |
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|
| 121 |
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"clusters_00_screenshot_09.jpg",
|
| 122 |
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"clusters_00_screenshot_10.jpg",
|
| 123 |
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"clusters_00_screenshot_11.jpg",
|
| 124 |
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|
| 125 |
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"clusters_00_screenshot_13.jpg",
|
| 126 |
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"clusters_00_screenshot_14.jpg",
|
| 127 |
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"clusters_00_screenshot_15.jpg",
|
| 128 |
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"clusters_00_screenshot_16.jpg",
|
| 129 |
+
"clusters_00_screenshot_17.jpg",
|
| 130 |
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"clusters_00_screenshot_18.jpg",
|
| 131 |
+
"clusters_00_screenshot_19.jpg",
|
| 132 |
+
"clusters_00_screenshot_20.jpg"
|
| 133 |
+
],
|
| 134 |
+
"analyses": [
|
| 135 |
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"mem-map",
|
| 136 |
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"clusters",
|
| 137 |
+
"clusters-00",
|
| 138 |
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"fluctuation",
|
| 139 |
+
"pca",
|
| 140 |
+
"rgyr",
|
| 141 |
+
"rmsd-pairwise",
|
| 142 |
+
"rmsd-perres",
|
| 143 |
+
"rmsds",
|
| 144 |
+
"sasa",
|
| 145 |
+
"tmscores"
|
| 146 |
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],
|
| 147 |
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"updateDate": "2025-07-23T12:45:47.758Z",
|
| 148 |
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"mdcount": 3,
|
| 149 |
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"mdIndex": 0,
|
| 150 |
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"mdNumber": 1,
|
| 151 |
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"refframe": 1,
|
| 152 |
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"internalId": "687fb4cfc2e28c32003cd987",
|
| 153 |
+
"creationDate": "2025-07-22T15:57:03.000Z",
|
| 154 |
+
"identifier": "A00GE"
|
| 155 |
+
}
|
data/files/A00GE/records.jsonl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
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data/files/A00GF/project.json
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| 1 |
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{
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| 2 |
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"accession": "A00GF",
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| 3 |
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"published": true,
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| 4 |
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"metadata": {
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| 5 |
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"NAME": "Dynarepo 7S11",
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| 6 |
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|
| 7 |
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|
| 8 |
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"Omid Mokhtari",
|
| 9 |
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| 10 |
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| 11 |
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| 128 |
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"clusters_00_screenshot_18.jpg",
|
| 129 |
+
"pocket_01.pdb"
|
| 130 |
+
],
|
| 131 |
+
"analyses": [
|
| 132 |
+
"mem-map",
|
| 133 |
+
"clusters",
|
| 134 |
+
"clusters-00",
|
| 135 |
+
"fluctuation",
|
| 136 |
+
"pca",
|
| 137 |
+
"pockets",
|
| 138 |
+
"rgyr",
|
| 139 |
+
"rmsd-pairwise",
|
| 140 |
+
"rmsd-perres",
|
| 141 |
+
"rmsds",
|
| 142 |
+
"sasa",
|
| 143 |
+
"tmscores"
|
| 144 |
+
],
|
| 145 |
+
"updateDate": "2025-07-23T12:45:50.189Z",
|
| 146 |
+
"mdcount": 3,
|
| 147 |
+
"mdIndex": 0,
|
| 148 |
+
"mdNumber": 1,
|
| 149 |
+
"refframe": 0,
|
| 150 |
+
"internalId": "687fb67704d3138edf21134f",
|
| 151 |
+
"creationDate": "2025-07-22T16:04:07.000Z",
|
| 152 |
+
"identifier": "A00GF"
|
| 153 |
+
}
|